Eagle's library interface is awful, I usually opt to just make stuff over from scratch whenever I need it rather than trying to move stuff from library to library, or trying to synchronize my libraries between multiple computers.
Also, their license options almost entirely alienate the hobbyist market. Their "non-profit" license is a slight step in the right direction, but it's still somewhat pricey for me; in addition, for the price, i'd rather have even more board space, and don't care about getting 4 signal layers. I'll NEVER spend $1200 on a full, unlimited license, and I don't see myself buying the non-profit license either. So really, by not offering any better options, they will never be seeing a dime from me. Eagle is a very common software package for hobbyists, I see it used everywhere, and yet they don't seem to want our business... I haven't ever heard from any other hobbyist who has actually bought a license from them... and I'm sure many of us who use it will never buy one because of the lack of options. If they offered a decent hobbyist license option, with quite a bit more board space (if not unlimited), 2 layers, and multiple schematic sheets, without any free tech support (so it wouldn't cost them anything to support it after you bought it), then no matter how cheap they made it (within reason) it would almost be free money for them, from those of us who would not have given them a penny otherwise.
Also, the annoyances that we put up with because it's free and powerful in a lot of ways seem to me like they would make eagle a poor choice for an engineering company that actually has the money to throw around for such expensive licenses. Also working against it is that it's not an industry standard like some of the more commercial PCB packages (protel, orcad, whatever)
I'm not quite sure who they're targeting... but it clearly isn't hobbyists, and they don't seem to be making any great improvements that would make it more appealing to real professionals with money to burn... Plus, by alienating those of us who are currently hobbyists/students (many of whom will soon go on to be professional engineers), they don't really give us much reason to consider using their product if/when we go on to be professional engineers and actually need expensive software packages.
With that said, I STILL haven't found a single free alternative that's any better, or even one that isn't free but is affordable. Seems like a rather important niche that nobody's filling. So for the time being and the forseeable future, I'll be sticking with eagle, and stuck with small boards for everything.