Personally, all of my future projects are going to be based around 3.3v. I really feel it's the more popular voltage range for embedded electronics. With ARM chips on the rise and working with 3.3v instead of 5v, I see no reason to continue to work in 5v.
I'm sure there are perks to 5v that I don't know since I'm still a newbie but it seems like the majority of components I'd want to use either only work in the 3.3v range, or work in both 3.3v or 5v.
As for your statement:
A 4 AA battery pack would be equivalent to 8 LiPos.
I think you are referring to the capacity ratings here, and in that case no. A 4 AA pack is most likely wired in series which means your capacity is not being increased. 4 AAs of 2000 mAh capacity each wired in series still gives you ~2000 mAh over all capacity, however wiring in series combines voltage so 4 AA in series is ~6v. So in this case 4 AA would be equivalent to 2 - 1000 mAh Lipos (wired in parallel not series) as for capacity. However if you only need 3v on the motors sparkfun has a 2000 mAh 3.7v Lipo that might be a better choice for you if you go that route: https://www.sparkfun.com/products/8483
you just need to make sure the discharge rate is sufficient on the 3.7v Lipo. It has a 2C discharge rate where as the 7.4v one you linked has a 25C discharge rate. If you convert to 3.3v arduino you can use another one of the 3.7v lipos for your arduino if you still want to keep the power supplies separate.
I found a nice explination of the discharge rates, as long as I'm understanding it correctly. 1C means the battery can discharge it's entire capacity in an hour, so a 1000 mAh battery that could discharge at 1C could provide 1000 mA for one hour. A 1000 mAh battery with a 2C discharge rate could provide 2000 mA for 30 minutes (or 1000 mA for an hour still). Going the other way, if a battery with 1000 mAh capacity had only say a .25C discharge rate, it would only be capable of supplying 250 mA for 4 hours. So the 2000 mAh 3.7v Lipos can supply up to 4000 mA for 30 minutes (or 2000 mA for 1 hour, etc). The 7.4v lipos with a 25C discharge rate would be capable of supplying 25,000 mA for approximately 2 1/2 minutes. So if your motors have more than 4000 mA current draw then the 3.7v Lipo would not be sufficient to power it.