Hi Neelesh,

Given the type of aircraft you're intending to equip, I'd go for the micro 12 along with 2 A123 2200 mAh batteries directly connected to the receiver without any regulator.
The feature/safety to price ratio of this combo is unmatchable ( bear in mind that you'll get one channel used for each battery )
I've been test flying my Phoenix that has 6 x 8411 ( main flight controls ) on that setup and the receiver is just doing fine.

Regarding the maximum current draw on the small unit, there is a trick. If you use two batteries, one at each side of the servo socket board, you'll be able to draw 4 amps from each side. So you'll have to plug one battery on channel 1 and one battery on channel 12. You'll then need to split and balance the big consumers ( servos ) on each side starting from channel 1 up and channel 12 down in a symmetrical way.
That will make it up to 8 amps which should be fine to cover most situations.

The programming capability of the micro is the same as the big R unit ( to the hardware differences ).
The and assignment and programmability of the channels is the same. However you cannot:
.Assign servo voltage by bank ( no on-board regulator )
.See the current draw
.Get the battery switch-over feature

Hope that this will help you...