Well, for the CRT, either configuration will get you about the same performance, since the 1y is a 2200 kv motor and the 2.5d is a 1700 kv motor; however, the setup with the 2.5d will draw fewer amps and run cooler (not that the setup will run hot with the 1y), at the expense of a bit more battery weight.

The problem is the controller. Some have had luck running the MM on 5S lipo, others haven't. It's a roll of the dice.

As for the smaller setup, the max I'd run on the 6900 is 2S. 3S will exceed the maximum rpms of the motor. I ran a 7700 on 3S and I couldn't gear it at all. The esc would just over heat. If speed is your concern, a MM with a 4600 motor on 4S would be the way to go, or even a 5700 on 3S. If you go with the 6900 on 3S, I think you'll have heat and gearing problems.

If you want the very best packs that money can buy, flightpowers and kokams are the way to go, in that order. Maxamps are good for the money, and I'm having good luck with the truerc 5S 8000mAh pack, which was dirt cheap, relatively speaking.