1. heavy engine criticals from a single faust or AT nade on a tank are an instance of the RNG just being too jumpy. It will often completely win one player a game.
2. German S-mines - does anyone use these? They cost way more than a minesweeper, take a very long time to set-up, and don't really do enough damage to stop people just walking or driving over them.
3. German sniper requires tender love and micro to get any use out of him regardless but thanks to his really low HP pool, he can go down in just a few lucky small arms shots, will die to a mortar shell landing anywhere in his vicinity, and frequently gets sniped by all sorts of things that shouldn't (like, an SU-85, for instance). Making his health that of a standard infantryman would probably improve the German sniper's viability in 1v1 a lot, while still not making him any more survivable than 1 shock trooper model.
4. Grenades are bugged all over the place. Riflenade warnings have been messed up and now come as the grenade hits, which makes playing against Grenadier spam require constant eyes on the units and even then quite challenging. Guard grenades and I think bundle grenades both frequently don't refund if cancelled.
8. Blitzkrieg on vehicles with engine damage seems a bit too much of a get-out-of-jail free card.
9. Some of the maps seem very favourable to one side or the other (so, Langres north start is pretty bad, Kholodny right is usually harder than Kholodny left, the new Kharkov one seems to be far better for the South player as well). I'm not sure to what extent this is underlying issues with the map layout and twe it's still people learning to try different things on the maps.
edit: added points I forgot at the time -
10 - T-34/85s are really underperforming for the cost on account of the very high reload time. Especially since the T-34/76 buff they don't really seem to match up. Has been adjusted both in terms of cost and effectiveness. They look OK on paper now. We'll see in practice.
11 - Flamer explosion criticals are very cool but they're also really problematic just because there's something like a 2.5% chance (I think it's 10% when the flamer model dies, right?) of an expensive muni investment vanishing on the first model that dies. The same problem doesn't apply to other muni investments like the LMG, which only drops on a squad wipe I think, or the DP machine gun, which can be picked up and recovered if dropped. I think it'd be a really good idea to make the flamer crit only have a chance happen if the squad is at half its models or less (so, when the second last or last combat engi or pio dies), to make this an element of the RNG you could work around. Has been adjusted to the level I thought it was from a higher level. Flamers have been improved against buildings. This may be fixed.
Generally, the game has come along a lot since release both in terms of balance and how it feels to play. Gj balance devs.
NB: Italicised points have been addressed. We'll see if they've been fixed enough as the patch meta develops. So far they seem to have been improved.
Updated, based on 12/11/13 patch