On the first point, the relationship is only 'clear' to us because it was the de facto standard since battle simulation began. Seasoned veterans can tell you most of the important numbers (speed tiers, important hp cutoffs, general IV spreads to barely avoid a specific threat with a general pokemon, etc.), because they're familiar with them. Newer players clearly won't have the benefit of that familiarity. The formulas used to calculate the various stats we use work just as well with level 50s as they do with 100s, or 75s, or any other level we so desire. A formula being set specifically at level 100 won't make any more or any less sense than that same formula at level 50. This actually stands as a mild rebuttal of your claim, as the older players who already know the current system would be at an advantage over the newer players who have yet to attain familiarity with it. Having both sides become accustomed to a new cap, together, would be much more suitable to the doctrine you mentioned.
On the second point, you are absolutely correct. In fact, any level between (and inclusive of) 1 and 100 is possible. Even more truthfully, certain pokemon shouldn't exist at level 50 (Dragonite, Goodra, Mewtwo, etc.). However, in the trainer battles on X and Y, both teams get capped to level 50. And that definitely does not conflict with the mechanics of the game, as it -is- a mechanic of the game.
On the third point, what potential is lost by having the cap at 50? You've seen the minor, trifling differences above. Moves based on the users level lose a slight bit of power, most moves in general gain a slight increase in power, speed tiers get a bit more interesting, Dragon Rage becomes a move worth consideration in lower-tier play. Where in that does a single pokemon lose all competitive viability and not retain even the -potential- to earn a spot on a team? Scaling levels doesn't affect the base stats of the pokemon in question at all: they merely scale them to the same level. A level 50 Mewtwo will dominate amongst a field of level 50s just as much as a level 100 Mewtwo would dominate against a field of level 100s. It's just how level scaling works.
And on the fourth point, I'm not exactly sure how Smogon handles it. However, we at Showdown! have always been looking to recreate the authentic battle experiences as accurately as possible. I could regale you on hours I've spent Metronoming both in-game and on Showdown! to see how certain moves interacted when chained off of it. I can't say exactly how we're going to approach this, as plenty of people enjoy the current standard of the lv100 cap. However, from the view of those who want to perfectly emulate the battle experience, moving the cap to level 50 will be a desired change, as that is what people will be seeing when they battle each other in real life, and likely how any Nintendo-hosted competitive events for X/Y will be handled.