Actually when you manually download something you shouldn't put in under content_download. Just put it under "Documents\OpenTTD\ai\". If that directory doesn't exist yet create it. You don't need to extract the tar at all.
I've placed it in the given directory (thanks for that Kogut) but after starting OTTD it still says AdmiralAI 25 is installed.
Maybe I'm missing the plot here, but I can't find a way to activate the latest version.
Putting the tar from that download in "My Documents\OpenTTD\ai\" works fine for me, putting it in "My Documents\OpenTTD\content_download\ai\" works as well. Did you restart openttd after you put the tar file in that directory?
@Samu: AdmiralAI doesn't "manually" replace vehicles, it uses autorenew. The behavior you describe (selling one train, buying a new one with a wagon more) is because autoreplace made the old train one wagon short. At some point that short train was not profitable enough, so it was sold. A bit later the AI determines it needs more trains for that line again, so it buys a new train (with the proper amount of wagons).
The large amount of trains waiting in a depot is clearly a bug. As you can see most of them have their depot orders changed to "stop in depot", that means the AI was going to sell them. I have currently no idea why it didn't actually sell them, but I'll fix that bug before releasing v26.
The half-electric route is easily explained: AdmiralAI will only convert rails to a compatible type (so only normal->electric, never normal->monoral or normal->maglev). When it wants to convert a route it just goes ahead and tries, if the route it too busy and it converting fails for too long, it'll stop converting and go on as if the complete route was of the old type (so no electric trains in this case). Later it may try to convert the route again, but that may take a while.
Thanks for your extremely detailed report after testing, it really helps.