I really would like the year of the film to be included in the name templating. I know its likely not going to happen so I've never mentioned it. I basically have accepted the fact that I will need to rename about 99% of the files I download.
Not to sound like a curmudgeony old man but here goes... The 0 padded season/episode numbers are basically an unwritten standard. It's more logical to use a predictable number of characters in a pattern. The pattern is the same unless a show exceeds either 99 episodes or 99 seasons, which would be rare. For the exact reason you stated,
having to rename the first 9, is essentially the reason to pad with zeros in the first place. Although this is almost the same flawed logic as the Y2K bug.
I would implore everyone to learn some form of shell scripting. Powershell is incredibly useful on Windows and now with WSL you can bash even. It makes handling these things trivial. You can attach scripts to logs, events, schedules, etc. to accomplish these tasks.
For example, after a download is done, you can drop it into one of two shared folders on a server. One will scale the video down to 720p and the other won't. So if its a video you don't particularly care to have the highest resolution you drop that in the 720 folder and it gets converted to HEVC at 720 with and stored in your Plex folders. That's just one example.
Scripting is really not that difficult. In fact, I think scripting should be a required course throughout high school and college, just like math or science. I've automated about 90% of my daily work tasks with Powershell. Linux shell scripting is even better. Your kids can thank me later.
Maybe a more useful feature would to be able to have the ability to trigger a script after download. Then we can make it do anything we need after AS is done.