It pains me to say it, but I finally had to give up on PokerTracker 3. Take what follows with a grain of salt, as many people love PT3 and have had no issues whatsoever, but I had serious problems with it from Day 1, and finally jumped ship to Holdem Manager when there seemed to be no real resolution on the horizon.
Just my two cents, but PT3 felt like it was released far too early, as the forums show many folks experiencing the same issues that I did, which were the HUD flat out not working and eating resources to the point that my entire system would essentially freeze up. You're going to have some minor bugs and tweaks with any major new release but that's a pretty fundamental issue, and it's one that impacted many people playing on a variety of systems on a variety of sites. When a beta/patch was finally released to address assorted issues, it actually created more problems for me than it solved, as the HUD was still not functioning correctly and the entire PT3 program started randomly crashing every 12-20 minutes.
I was a big fan of PT2 and loved the support and quick action on any issues that cropped up, but that definitely wasn't my experience with my PT3 issues. Two of my support tickets have been unanswered for weeks and they're still actively selling licenses for a product that is non-functional for some users. I'm completely guessing here, (and too lazy to do any investigative legwork) but it feels like someone bought the original product from the creator at some point in the recent past and is a bit over their heads in general, releasing it too early and unable to quickly address some of the major issues cropping up.
But, like I said, your mileage may very. Lots of folks are tickled with PT3 and it's working flawlessly for them. I unfortunately wasn't one of them. If you're on the fence, it might be better to wait a few months before moving over to PT3, as I imagine they'll get many of the kinks eventually worked out that some users are currently experiencing with the product as it now stands.
As far as Holdem Manager, I'm more than pleased so far. It's not as slick and finished looking as PT3 but I've had no performance issues at all, it's got tons of stats and filters, graphing functions, integrated HUD, all that good stuff. Not the prettiest or slickest software but so far it's fast and it flat out works, which is all I'm really looking for.