First of all, the weapons unlocking system. I admit that in theory this system is a lot better than the achievements, but it's a shame it doesn't work. Lady was playing for four hours last night, and she didn't get a single weapon. Nice work Valve. I've been playing for seven and I only have one (admittedly, it is the huntsman which is just the boyo).
Secondly, a lot of the maps are broken. Especially the arena maps. Nucleus seems to have a problem with half of it's platforms being classed as "Solid", meaning you fall through things a lot and for some reason none of the unlockables work anymore on arena maps.... Typically.
When you overlook the flaws however, what you have here is a very ambitious update that offers a lot to new and old players alike. So good work Valve, just release a few patches pretty quickly yea?