Having bigger counterlungs is not an issue once you get some hours. You should be running minimum loop volume anyway. It's at the beginning where it's easy to put too much gas in the loop and you start dealing with buoyancy issues, etc. It just takes a little more effort to dive. Having counterlungs that are too small however, can cause all sorts of problems. Ideally you want the right size, but if you have to go one direction, having more space (that you won't use) is better than not having enough space and making it hard to breathe, triggering the OPV all the time, having to vent, CO2 retention, etc.
That being said, diving with massive lungs has its own set of issues. I HATED the stock counterlungs on my Meg because they were so big, but as soon as I went to neoprene lungs it was much easier to dive. However, if the neo lungs were any smaller, I wouldn't have been able to dive it safely at all. It's all a tradeoff.
You need to make sure you can adequately vent your lungs so that you don't start to retain CO2. If you can't do that without pissing gas out of the unit, your counterlungs are too small. Once you get the hang of minumum loop volume and you're comfortable, the excess size won't matter and you can step down in lung size if you want.
I'm not a rebreather instructor, but this has been my experience on the 3 units I'm certified on, and the several I have try-dived, including the waffle box.
As for what specifically to look for, ask
@Dsix36 he's probably the most knowledgable about what things you need to look at, he's had his apart, butchered, frankensteined, put back together, subject to some questionably ethical studies into machine sentience, and all points in between. He probably knows more about the units than Paul does.
Sorry for hijacking.
