Mongo was built with horizontal scaling in mind, and to that end, it tends to suffer noticeably when you overload a single node. Things like the global write lock and single-threaded map/reduce are definitely problems, and shouldn't be pooh-pooh'd away as "oh, just scale horizontally". Uncompacted key names are a real problem, and a consequence of it is that Mongo tends to take more disk/RAM for the same data (+indexes) than a comparable RDBMS does. Maintenance is clunky - you end up having to repair or compact each slave individually, then step down your master and repair or compact it, then step it back up (which does work decently, but is time consuming!)
None of these are showstoppers, but they are pain points, especially if you're riding the "Mongo is magical scaling sauce" hype train. It takes a lot of work to really get it humming, and once you do, it's pretty damn good at the things it's good at, but there are gotchas and they will bite you if you aren't looking out for them.