1. Im definitely for implementing this, even solely for the pugs sake. Shame to see 170 people signed up and only 20-30 people pugging. It also gives at least some info about player's current skill, however, playing 3-5 games if you've been inactive for a long time won't bring your skill to maximum so the data will still be incorrect in some cases. But of course, nothing more can be done there. If players don't wanna show their skills, they won't and most can do it knowing they will get drafted 100%.
2. There is a side of me that likes the feeling of safety in such fallback-d sided maps, but it just doesn't function anymore. Choosing offense sided maps and creating new maps with less open areas (less chances of shooting someone you missed) doesn't only aid to the turtling problem but also brings more pugs because people need to learn them. So yas pls!
3. OMG YES!!! So much more fun to be had and fallacy's suggestion is great. Kevinsanity does bring a valid reminder that that way 1 player from the lineup cannot play but that player will survive it

And that player can always be switched with someone else and that player can always pug more other mods to become better and recognized in them.
4. I assume the problem with dev matches with 24 teams would just be the amount of games that would have to be played which brings some obvious problems. Umm well, as you said, same amount, if not probably more, players will play ( in 24 teams there is more chances, overall, for someone in starting 5 to miss a week, while at the same time that person will mostly be easily replaced) while it fixes skill concentration issue. So yeah, definitely a go as well. Still, a problem of many players not playing remains. Getting them to play would take a lot more work, like for example organising another smaller division matches with play offs, maybe even on another day without streaming or supervision. I mean i could be wrong but i think people would be satisfied just to play and get their results on The page. The winner can also get a spot in 1st division as a reward for the next league. If im wrong though, there is not Enough interest of weaker players to play and thus being one of them who has it really sucks, but there is nothing else to be done.
About captains, if there will be problems, consider my suggestion of 24 low salary captains with a promised spot in the line up. Now does it have to be 24 of them or you can just fill the empty spots, idk. Depends on what will an average 5th of good-captain-teams be.
5. OMG OMG YES YES

bug mentions camping in lms getting a little out of hand and then gives a good fix but probably not doable because of the available commands in a mod? Imo, it's just easier to have everyone's health drop with time from the beginning and gaining health on kill, as is already done in the only currently alive (in a coma) lms server. From personal experience it works great, but at the end a camper will always have more lives compared to someone who went on rampage. Thus health drop needs to stop with last 2-3 players remaining to avoid ability of camper to keep running away.
About MCTF, i'd even like us to have a little announcements of when few people would like to pug it.One of the reasons that game doesn't start as much is because no one really expects another 11 people to add. So 8 people saying on forums that they would like to play then and there could help.
TL DR: ONE BIG YES!