I think the sieges are ok but definitely agree on agent spam. My counter now is to actively go hunting agents with mine and tbh it's been far less of a problem since!
On the battles, I actually enjoy that, I pause battles occasionally to survey the current weak spots and react accordingly whilst setting up powers etc.
If you are not fond of those pesky agents, try looking here for a good mod which will limit their effectiveness:
http://steamcommunity.com/workshop/browse/?appid=364360&searchtext=less+op+agents&childpublishedfileid=0&browsesort=textsearch§ion=home
I have both mods and they are very good indeed.