My opinion
I personally don't feel shoe games are any harder to count than pitch games. Counting is counting to me. Of course the TC conversion is different, but more mitigating factors are casino heat at pitch games. As far as losing the count, which I think we all do sometimes since we're human, in a shoe game I don't stop counting and wait for the shoe to restart. Being off by +/- 1 seems to be pretty inconsequential. It's more important near the end of the shoe, but still doesn't have that much effect. Worse case, I am slightly underbetting if it's higher than I think it is. I might be playing slightly longer if it's lower, but I typically wong-out in negative shoes. Of course in pitch games this is greatly magnified. If I lose the count in these situations I just flatbet playing BS knowing it will be over soon. But because it so short this rarely happens and is probably, inadvertantly, good cover when I do. I don't keep a side count of Aces, but I have read many different ways of doing so (i.e., pointing your feet in different directions). I thinking creativity is the watch word here.
There are other more knowledgable people that can speak specifically about the "dilution" of the count. From what I understand it's all the same in the long run. I have had shoes where the count went skyhigh from the very beginning where eventually the TC was in the +10 range. But as far as justifying a "non-minimum bet" this is done at TC+1. If your waiting for really big TC's then your probably not spreading big enough. If you're used to playing pitch games, this may be the most difficult for you. You need at least a 1-12 spread to beat a shoe game. (I assume you know all of this already, but for the sake of other readers I'm staying pretty basic.)
Penetration is everything in any game. I would play a 4.5/6 (75%)shoe game before I would play a 50% 2D game. When that count does go skyhigh I want every opportunity to see those cards. Dealing only one deck out of two yields so fewer opportunities than the shoe game with a bigger spread. 5/6(83%) games are out there and if you add LS it a great game. I like the quickness of pitch games and didn't focus on shoe games because of the time it takes sitting through a shoe that stays neutral. Now I play whatever I can to get the hours in. It's all about spending "quality time" in your friendly neighborhood casino.