Project suggestion!

Hey,
I need some project idea for my academics. I'm Electronics & communication engineer. So please suggest me nice micro controller (with or without Arduino). Its for my academics so please suggest a nice one.
Please do help!

Since this is an Arduino forum why not try Arduino, UNO Rev3 is a great choice.
How far have you gone in writing software and electronics design?

Why don't you start with what interests you...

I cant use ready made boards available. I have to etch it. About programming well, i cant write a code after a few trial and errors

Ok then download the arduino schematic and etch your own board. The Arduino teams allows people to modify their design to come up with new board ideas.

Plenty of standalone designs have been posted here. Find one of those, and use a standalone ICSP programmer to put bootloader code into it.
example:

Then use standalone USB/Serial adapter for debugging via Serial Monitor/USB port.
example:

Put header pins on your board so you can plug these in directly.
You can download sketches with just the first, but you don't get the USB interface then.
You can't download the bootloader with the second one.

What to think of a board that can harbour 1 to 4 328's that are connected through the I2C bus (1 master rest slaves) but have the rest of the pins free.

sort of distributed node with max 40 IO pins max 20 ADC lines max 10 PWM or so.

So something like 2 of these?
Schematic here
http://www.crossroadsfencing.com/BobuinoRev17/
Outer pins are almost all GNDs, leave off if don't need.
20 IO/chip - 6 can be ADC, 6 others can be PWM.

I've designed a Dual '1284P board as well. Haven't ordered any.
32 IO/chip.

yep