Actually, Kirsch came in for season 7 as well, part of closing down the X-Files and all. The one thing I liked about him was the way Mulder's reactions to him were written, between that and Duchovny's performance, it added a nice dynamic to the show.
Kersh actually first appears in season 6 and he doesn't appear at all in season 7 until he was brought in to be a kinda nemesis in the Doggett era.
I remember watching the DVDs first (I actually tuned in to the first episode when I was a kid the first night it aired and for whatever reason I didn't continue watching) and having some basic knowledge of what was going on on the show. The DVD releases began right around the time there was all the drama with Duchovny and the casting of Robert Patrick and even though I tried keeping away from the new episodes (I wanted to watch them in order with minimal spoilers) I'd still catch an ep here or there while flipping around or come across something about a new ep online and I saw that Kersh played a significant role in that era.
When I got the DVDs and I saw him in season 6 I thought he'd be a steady presence in the series from that point on and when I got season 7 a few months later when that was released I was surprised that he was altogether absent from the show for an entire year. When he finally reappears in season 8 they sorta make a point of addressing it though, I don't remember exactly but I know they sorta treat him like a long-dormant threat that's resurfaced.
In any case, I'm a fan of the whole series and I'd like to see a followup to the finale in 2012 but they really didn't leave much to work with in regards to characters. You have Mulder & Scully on the run, and Skinner, Doggett and Reyes are still at the FBI but you have a huge chunk of the fanbase that hates D&R, you have almost every other character dead, one of the last two surviving nemeses (Kersh) suddenly turns good and the other one (Toothpick Man) never really had the opportunity to develop as a character and is certainly unknown to most viewers. You also have Jeffrey Spender and Baby William (who would be 10 or 11 at the time of the invasion) still hanging around but that's still a far cry from CSM, Krycek and the Lone Gunmen.
I think we'll get a "prequel" type movie with this one, like a crowd-pleasing "lost episode" that allows them to include all the dead characters (I've heard rumors that it takes place sometime during season 7) and hopefully that is a success so they can ride the wave of that success into the big 2012 alien invasion spectacle.
I think they could make the alien invasion exciting enough so that people could swallow the fact Mulder & Scully are no longer FBI agents and only Skinner, Doggett, Reyes, Kersh, Toothpick Man, Jeffrey Spender and Baby William could return.
