This is based on what I've seen so far. I have not played every map in every mode yet so this list is far from comprehensive.
1. Crucible and exile in conquest mode take way too long to finish games. This is because the positioning of the health crystal makes it impossible to push into their base unless you're so far ahead in terms of items and levels that you can kill them at the crystal.
2. On exile in fortress mode, the start of the game consists of sitting in your lane and killing the creeps. Your warscore is a given because the one flag you've got to keep safe is protected by a long row of towers. This makes it a boring mode to play in(in fact, the general lack of flags makes fortress mode pretty bad on all maps).
I'm sure there are many other modes on various maps with similar problems. Please list them and bitch about this stuff so gpg can fix them. In order for Pantheon and Skirmish to really work well, the maps and modes it selects need to be fun and playable. Obviously there are more important issues at the moment, but maybe if we bring this up now we'll get a fix for this stuff immediately following things like the connectivity and favor points fixes.