To me, the biggest issue is filter lists can only be updated when the extension updates and Google controls the update cadence. YouTube ad blocking, for instance, requires frequent filter list updates (or did a few months ago, I'm not sure where things stand now).
TL;DR: In order to detect ad blocks sites create "bait" URL's that look like ads, but are purely there to detect if ad blockers block them. The only reason to do that is to punish the user for using a ad blocker, perhaps by nagging them, perhaps by refusing to display or load the content entirely. UBO responded by making bait URL's appear to work by redirecting them to local resources. Sites responded to that by putting required content behind bait URL's. So UBO now uses a number of dynamic heuristics it uses to detect what is bait and what isn't. Those heuristics aren't possible in V3.
My guess is UBO ability to change it's behaviour for every site based on what the site did created never ending war between ad blocker detectors and UBO. Engaging in that war too much effort for a lot of web sites to engage in, which is why you don't see too many ad blocker detectors. With advent of V3 this dynamic will change, as UBOL will have one hand tied behind it's back. My prediction is once V3 comes in, a lot more sites will start demanding you disable UBOL - but they won't notice the presence of UBO.
To me, the biggest issue is filter lists can only be updated when the extension updates and Google controls the update cadence. YouTube ad blocking, for instance, requires frequent filter list updates (or did a few months ago, I'm not sure where things stand now).