I'm gonna go ahead and agree with Tesung here in that the problems with BP more or less isn't something that you can just blanket fix altogether. I'm gonna speak on Gen 6 since that's really what I've become accustomed to as far as my time here on Smogon as a competitive player.
Generation 6 Baton Pass, as far as OU is concerned, is extremely obnoxious at times. It's obnoxious because it allows a passer to pass to something that is already considered the pinnacle of a team and just enhances it further to extremely high levels. Under most circumstances though the obnoxious characteristic of Baton Pass are generally in a combination of two stats, an attack or special attack stat + speed stat. Nasty Plot Celebi + Rock Polish M-Diancie is just one example of this. This example is more or less where people will come from in regards to blanket banning the move, or at least from my perspective this is one prime idea of what a lot of people refer to for blanket banning the move. I personally, think this is ok to an extent. It might be realistically annoying to face and somewhat mindless but it still requires a legitimate thought process to pull off successfully if we're going to assume the two players are capable in a relatively higher capacity.
Smashpass + Kyurem-B is another example, one that is rare but is what I'd consider what would start to push the boundaries of an acceptable use of Baton Pass. You're applying twice the stat increase on a Pokemon that has the ability to ignore other abilities, thus invalidating about every playstyle in one go if played correctly. Outside of priority, which probably won't do the trick either most smashpassing + Kyurem-B strats will use all out attacker with some bulk and with HP Fire making Scizor a liability, chances are you're gonna lose to this considering how these teams are actually built with screens, supplements, etc.
GeoPass breaks the threshold completely in my eyes, to the point that arguing that it holds any sort of real competitive value is a lost cause. I'm going to go out on and limb and say that the nature of these teams and or playstyle is an inherent problem in that anything being passed more than three stats is more than likely going to just break the game in that very instance at that point, by breaking I mean whatever chance the opposing player facing BP had barring matchup and luck. This is the main reason or what I assume it is as to why it's such a problem in Gen 6 so I don't think there is a necessity to go any further.
Who isn't aware of GeoPass at this point? Denisss made a RMT about it and it's been used by a TON of people on the ladder for fun or brainlessly achieve reqs during Suspect Tests. It now sees Tournament usage. The OU Council plan to take action towards GeoPass soon enough.
Replays:
http://replay.pokemonshowdown.com/smogtours-ou-53719
http://replay.pokemonshowdown.com/oususpecttest-152706284
....many more...
How to get rid of this: Ban Geomancy or Ban Baton Passing more than 2 different stats boosts (if possible)
My personal opinion, I wouldn't mind seeing a blanket ban of Baton Pass as far as Gen 6 goes. Let's face it, another loophole is going to be found when we do another complex ban until that happens or we start banning Baton Passers, which may sound ridiculous but Smeargle's position in BL at this moment is due to its support characteristics in supplementing receivers who would otherwise be not broken or manageable under normal circumstances, same deal with Combusken for NU this gen. More than likely smashpass will just takeover and we all know it's supplemented by screens, tailwind, a bunch of support stuff that does turn games into an inherent matchup issue that individuals have stressed about. If anything though you'd more than likely would have to combine the two proposals you stated McMeghan, trust me this generation and pool of players is a bit more creative in exploitation of strategies than the proposal is giving them credit for.
I can't speak on older gens but again, general clauses for issues like these apparently aren't the way to go about handling this, seeing as how it was attempted twice in Gen 6 but people still manage to exploit loopholes.