Well, the problem is that their availability is notoriously late. While they do destroy, it's generally accepted to put late legends into A-tier and that's how it is in most tier lists (e.g. Rayquaza in Emerald would be a clear S if it wasn't for the fact it comes after 7 badges). I can see the point, given they are more self-sufficient than the rest, but S-tiers, in addition to being consistent, also do not come very late (Jynx still comes before 4 badges and has traded Exp. as a compensation somewhat)I would invite you to reconsider the birds though—at worst it's one Silph Co. and one Koga later, and then you take five minutes to grab them with the Master Ball, and you have a level 50 legendary bird with opponents like Sabrina still left to fight)
Also, I am interested in the idea of a "no TMs" list vs "TMs list". I also noticed that things like Paras need SD and Dig and because both of those are very contested TMs, Paras becomes utter trash as soon as you teach them to something else. If we put Paras at C, for example, or whatever tier you want, it doesn't matter, due to those TMs but the player has already picked a teammate that uses SD + Dig (say, Charmander), the list loses its usefulness (tiers are very good way of quickly telling the reader how good a Pokemon is compared to the rest of the Pokedex), as the list does not "rank" the Pokemon on its own worth.
I'd say, if we were to do something like this, we should only allow the Department TMs, as those are rebuyable and thus anything can use them. We probs should limit all one-time use TMs (more specifically: Ice Beam, TBolt, Blizzard, Body Slam, Psychic, Dig, SD, Earthquake, and some others that I cannot think of). GC TMs are reusable but you are reasonably getting only one, so it enters the category of one-time use TMs. It does raise the question of why we are limiting some of the less contested TMs like Mega Drain, but limiting them all would be more consistent and less arbitrary. It does mean that stuff like Clefairy become a lot less viable (in fact, auto E-tier), but at least players that have already used up their TMs or want to use them on something else will know that Clefairy is utter trash without them
Another con with the idea is that it is highly likely to kill off any chances of this being released, as this'd be a lot of work to do for QC and GP (given they are doing 2 lists, not one). Though they can be made so that both lists are on one page and toggleable with a button (I am part of the HTML team so I can easily do it, if I were to HTML it). There are also a lot of questions to answer (should we have another thread for this? Should Drumstick lead both of them? Should self-sufficiency be ignored in the TMs list, now that the TM list doesn't care about competition? etc.). All in all, I think the idea could work, but it's probably something we gotta discuss first and answer all questions before we proceed with such a major decision.
Another idea is just to not weight competition against a Pokemon and be very clear in the Pokemon's write-up what trash it is without some of those TMs. (e.g. "Clefairy is one of the best Pokemon to use for RBY if you teach it the aforementioned TMs. Clefairy is very bad if it doesn't have access to any of them") or something like this. Less work to do for everyone, no need for a second list, but less useful to the reader, as they don't get a ranking, but that's probably what the majority would prefer as a whole.