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Is there any alternative ways to create communication between Android and Computer via USB but not using Android Debug Bridge?

I want to send and recevice data between .NET application and Android Device by using USB. However, due to the security concerns, I do not desire to use Android Debug Bridge (USB debugging).
Is there any possible way to send and receive data from Android Device to my .NET application on computer by using USB ?
Thanks in advance.

There are many ways to skin this particular cat, let me name two:
Simple message files via MTP. Pro: Easiest to implement and widest possible client support. Con: High latency. Good, if you have few requests with a bigish payload each.
USB networking via CDC-ECM. Pro: Allows easy extension to full networking. Con: Not so broad client suppoort. Good, if you have full control over the hardware.
The prevalent problem is, that the fragmentation of Android allows you to assume only a very low baseline.
I do recommend, that you revisit the encrypted network connection option: It should be quite trivial to create a minimal network consisting only of the Android device and a single partner - e.g. by pluging a WLAN access point directly into a secondary network interface of the workstation - and by being associated to a special WLAN you make sure, that the device at this point is not connected to a different WLAN or mobile network.
This will not only be easiest, but also give you the best starting point if you want to upgrade to a broader network later on.

Transfer data between iOS and Android via Bluetooth?

I've been reading up on how to transfer data between iOS devices over Bluetooth using GameKit. I'm not writing a game, per se, but do have a need to transfer a small amount of binary data between two devices. Between two iOS devices, this is easy enough. However, I was wondering if it is possible to transfer data between an iOS device and an Android device via the same mechanism.
Has anyone come across documentation/tutorial that would explain how to do this? Is it even technically possible? Or has Apple put in some sort of restriction that would prevent this?
The other option I discovered was Bonjour over Bluetooth. Would this be a more suitable option for this type of operation?

This question has been asked many times on this site and the definitive answer is: NO, you can't connect an Android phone to an iPhone over Bluetooth, and YES Apple has restrictions that prevent this.
Some possible alternatives:
Bonjour over WiFi, as you mentioned. However, I couldn't find a comprehensive tutorial for it.
Some internet based sync service, like Dropbox, Google Drive, Amazon S3. These usually have libraries for several platforms.
Direct TCP/IP communication over sockets. (How to write a small (socket) server in iOS)
Bluetooth Low Energy will be possible once the issues on the Android side are solved (Communicating between iOS and Android with Bluetooth LE)
Coolest alternative: use the Bump API. It has iOS and Android support and really easy to integrate. For small payloads this can be the most convenient solution.
Details on why you can't connect an arbitrary device to the iPhone. iOS allows only some bluetooth profiles to be used without the Made For iPhone (MFi) certification (HPF, A2DP, MAP...). The Serial Port Profile that you would require to implement the communication is bound to MFi membership. Membership to this program provides you to the MFi authentication module that has to be added to your hardware and takes care of authenticating the device towards the iPhone. Android phones don't have this module, so even though the physical connection may be possible to build up, the authentication step will fail. iPhone to iPhone communication is possible as both ends are able to authenticate themselves.

Maybe a bit delayed, but technologies have evolved since so there is certainly new info around which draws fresh light on the matter...
As iOS has yet to open up an API for WiFi Direct and Multipeer Connectivity is iOS only, I believe the best way to approach this is to use BLE, which is supported by both platforms (some better than others).
On iOS a device can act both as a BLE Central and BLE Peripheral at the same time, on Android the situation is more complex as not all devices support the BLE Peripheral state. Also the Android BLE stack is very unstable (to date).
If your use case is feature driven, I would suggest to look at Frameworks and Libraries that can achieve cross platform communication for you, without you needing to build it up from scratch.
For example: http://p2pkit.io or google nearby
Disclaimer: I work for Uepaa, developing p2pkit.io for Android and iOS.

You could use p2pkit, or the free solution it was based on: https://github.com/GitGarage. Doesn't work very well, and its a fixer-upper for sure, but its, well, free. Works for small amounts of data transfer right now.

Passing values from an android device to another

Is it possible to pass a value from an android device to another? I mean, without using the Internet. My project will be implemented only on a localhost. The two android devices are only connected through the router. If it is not possible on the local area network how can I do this? Are there other ways? I'll use the Internet or any other options if possible. Links to open source code, if you have any particularly regarding on this topic, would be appreciated too. Thanks!

If your target is Android4.0+ you can use wifi direct as #pgsandstrom stated.
In other cases if you want to make client/server comunication with two android decices you should look at this thread Socket Server/Client with two Android devices and the awser to this question may be usefull to you too How to write an Android SocketServer to listen on wifi.

If you can restrict usage to Android 4.0 or later, then have a look at wi-fi direct. It doesn't use a router thou, so I hope that isn't a restriction. If you need to support older devices, I think you have to go with bluetooth.

controlling Embedded system from MOBILE. ANDROID or iOS? suggestions and explanations please

As a part of feasibly study. I need to choose between Android or iOS for integrating it with an embedded system.
Basically, that embedded system will have an AVR or a PIC Microcontroller. I want to establish a communication between a mobile and that particular system.
Need some wireless technology for communication (bluetooth,wifi,internet etc..)
Micro Controllers have communication ports like UART, USART etc..

It really depends on the kind of communication you need.
I particular, if you have a normal WIFI connection and your controller can work with receiving & sending your data via wifi, you may go iOS or Android.
If however you need some kind of free format serial communication, you need to go Android, serial cable via USB.
recarding other factors, I guess it really is just a personal taste issue.
Could you give more info on how & what needs to be communicated and what kind of communication device you have between your phone and the device itself.
Not sure if this is similar to what you have in minde, but you might look at this: http://www.arduino.cc/ being probably the best known example in this context.

Using some serial to bluetooth module would be the most easier to implement.

I would go with Android unless your target audience are photographers. Seriously. Also, with iOS you need to be careful. For instance you want to use BlueTooth, but not all iOS devices will connect to, say, the Bluetooth protocol for a keyboard. (Ah! You didn't know there were more then one Bluetooth protocol did you?) And I don't think any iOS device will let you connect using the Bluetooth serial port protocol.
With Android you can jump in and start flying immediately by using the (or a copy of) the PIC 24F based IOIO board. And if you are an Android / Eclipse developer (I think) you can down load and use the IOIO JAVA / Android libraries. I have been told this makes programming the IOIO board just about as easy as programming an Arduino. Especially if you are well versed in JAVA, Android and the Eclipse editor. Add to this the IOIO board can be a host to the Android (i.e. connected by wired USB) or host to some Bluetooth modules (i.e. connect to the Andoid's bluetooth radio).
If you don't want to go it along you can buy the Microchip Android Development Kit (ADK) board which is also a PIC 24F based "USB wired" using AOA protocol to connect to an Android. I say "not going it alone" as I would expect you can then get limited support from Microchip w.r.t. their hardware (the ADK board), software (Android) and firmware (PIC ADk board). This solution, however, does not have built in Bluetooth support. I am guessing you can add it, it's just not part of the ADK software/firmware that Microchip put together.

How to utilize network for p2p file sharing on Android Platform?

I'm working on some apps for the android platform and I have two problems that I'm not quite sure how to approach, and both are closely related.
How can I send a relatively small data file from one android device to another (preferably over the internet or directly through wireless network)?
Is it possible to create a temporary p2p live data stream from one android device to another? An example application would be to stream low-res video from phone A's camera to phone B, or audio.
I would much appreciate being pointed in the right direction on either issue (File transfer or real time data transfer).

You could try to get Google's library libjingle to work on Android. It provides quite advanced NAT Traversal capabilities, which should be able to get through the carriers' firewalls.

One approach would be to use the socket classes in java.net.

To use WiFi to send data among devices, you can try to establish an ad-hoc network among the devices that will communicate. I think you can use Android's WiFi API to do that. Once you have the ad-hoc network setup, you can establish a simple TCP connection between the devices and transfer the files.

Sockets do not work between phones. I've tried with two actual phones using socket communications and there seems to be a firewall in the carriers that prevents communications on ports different than port 80. Then if you try to use port 80 you get a 'Permission Denied' exception.

One possibility is to investigate the JXTA framework. The Practical JXTA II book is available online for reading at Scribd.