I think you make some great points, to which I would say:
1) metagame design is hard. If this site is bad at it, probably part of that can be attributed to the fact that I'm not particularly good at it.
The big challenge is that much of our design is still anchored in power-max philosophy. We chop off a lot of GRBS, make fixing way better and then push the hell out of everything else. To do anything else requires a complete change. There's no breathing room at this point in the power curve.
That's not to say there aren't dynamics. We all put in more exile cards to fight gravecrawler et. al.. We put in Wastelands to fight the improved fixing. More sweepers to fight the improved aggro and lack of Wurmcoil Engine.
But to really develop a metagame? To think like a designer? I need to step wayyyyyy back on the power curve. Or design my own cards. Or do something else.
Part of what defines limited formats is a push in some direction. The bulk of the creatures in Scars of Mirrodin were soooooo small that Arc Trail generally agreed to be better than Koth. The Eldrazi formats are so cluttered with little tokens that the top-end guys need Trample or an attack trigger to be a sufficient reward for bothering to ramp. Landfall guys are shit on defense, so blah blah blah.
This whole metagame thing needs a stimulus. It needs a push in some weird design direction. Every time I modify my main cube to push in some direction (zombies, lifegain, pod), I try to provide players with some counterplay. There certainly could be more attention paid to things like critical toughness, but I think in the context of a "generic" Riptide style cube, there's not much of a stimulus.
BFZ is interesting because most of the removal doesn't just let you unconditionally destroy something.
Gideon's Reproach can't kill a big guy without chump blockers. The red spells can't unless you stack or have a ton of lands for that
spell.
Sheer Drop lets the opponent get an attack off first, but you can counter this with things like the land that grants vigilance (or by not attacking).
Smite the Monstrous does it, but it's just one card, and you can try to force them to use it on a smaller target.
Stasis Snare and
Quarantine Field can, but they are less common in the environment.
Unique mechanics enable this, as does the breaking of singleton on removal. Lower power allows us to include more conditional removal.
I think these ideas are good, and underdeveloped, but it's really hard to get there, and with full honesty, I don't know what I can do with these ideas to apply them to my primary cube.