Championships have changed through the years. The first FSU win was in 1993, and who gets to play in the Championship was determined by the Associated Press (they'd rank teams).
Later on FSU went to three straight and won one of them (was the late 90's), and by that time college football had switched to the BCS system, and the BCS chose what teams deserved to appear in the championship.
Finally, back in 2013 FSU won a third time, and that was the last year of the BCS. Since then it has changed to a playoff system, where a committee ranks the teams and the top 4 are placed in a two game tournament. FSU made the first one in 2014 but lost, and they've not been back since.
The Associated Press still provides rankings and they're followed for the first half of the season, but somewhere around week 7 or something the playoff committee starts issuing their own rankings, which are the only ones that actually matter as far as bowls and playoffs are concerned.
Really, FSU could have still made the playoff this year despite the opening loss if they ran the table, and they looked good enough to have a shot... but the loss of that QB has really put a damper on that. At this point they'll be lucky to put together a 3 loss season and make a major bowl game.
Determine the top teams and who plays in bowl by a poll sounds pretty shady. How what teams play in what bowl game doesn't really make much sense to me. I really wish college football had it's own March Madness. It doesn't really seem like there's a true national champion.
They'll need to smack around the rest of the opponents, but if the top quarterback is injured it's probably not the most likely.
These days the "New Years Six Bowls", which are essentially the top bowls (it includes the playoff matchups), are determined by the Playoff Committee's rankings, and the committee is very upfront and forthcoming with their reasoning. So far it has worked rather well.
The many, many other lesser bowls, though, all have their own considerations... some are promised to the best available team from one conference or another, most of the lower ranking ones take proximity into account to maximize attendance (meaning a bowl in georgia is more likely to involve southeastern teams), and in general it usually works out fairly well simply because there's so many of them lol; if you finish the season with a winning record, you get to go to SOME bowl.
It was never very "shady" before the playoff committee, just controversial. The BCS system, for instance, was decided by an algorithm, and many people were frustrated that it was missing developments that humans could see. Prior to that when the Associated Press would determine the champion, there were definitely times where bigger names likely benefited from their fame in the rankings and there were actually years where multiple teams claimed the championship lol
The current system is definitely the best one we've had so far. When you have a league involving 128 teams and the season only lasts about a dozen games with most taking place within the same general region against their own conference, there is no perfect system for somehow determining the best four of that group. Fortunately though (and this is why the change to a four team tournament rather than picking two teams for a championship is better), by having four slots it really helps ensure that the best teams aren't getting left out. So far it has worked quite well, and I like the system for the most part. With a game as expensive and physical as football it's really not realistic to expect a larger tournament (teams would be tattered by the end of the season); I imagine the biggest it might ever get is an 8 team tourney, but it'll probably remain 4 teams for the foreseeable future.