While I did my first playthrough in turn-based mode, I switched to real time for the second one and stuck to it afterwards. The balance is completely different obviously, and the issues you've mentioned may be a result of trying to balance the weaponry to both modes. What I find lacking is a wider weapon selection allowing for further tactics. For example, a one-handed alternative to the machine gun. It is particularly visible on the aliens' side (though perhaps it would be too weak, since it would have to be weaker than the disruptor), but it applies to X-Com weapons too - both pistols are not exactly the same thing. Shotguns would be nice too. And I think I really don't like effective lack of burst fire. I'd really prefer if the X-Com mechanics were used: various weapons have roughly similar times to fire in aimed and snap modes, and the autofire has a set number of bullets that are sprayed in a short timeframe, costing a lot of TUs. Of course this could make point-blank shots too effective, but I think it'd work.