Yes, Monk Stances are a big problem. I can see two likely outcomes:
1. Put them in Henshin. It makes sense lore-wise, but would be awful for multiclassing monks. It also means that all Monks would be putting points (and quite a few of them) into Henshin, since the stances are just too good to pass up.
2. Split them among the PrEs, as you suggest they might do. But what goes where? I'm not so confident that Ninja Spy would get Earth, since Ninja Spy is the Developer Designated "Rogue-ish" PrE, while Earth is the Developer Designated "Tanking" stance. Fire, in spite of its mechanical affinity to Ninja Spy, strikes me as a Developer Designated "light" element, especially given the Jidz-tet'ka bonus. I expect Wind to go to Ninja Spy (Dex going to the Rogueish PrE). Water is hard to say, but given the Jidz-tet'ka "poison" bonus, Ninja Spy makes some sense. I really have no idea what Henshin would get. Maybe Fire (given Oremi's set), and Water (just because the worst stance would inevitably be one of the ones that gets duplicated)? I think all of this is a very bad idea, though, as it shoehorns in certain combinations of PrE and Stance.
So, what do I think they should do?
Simplest option (at least conceptually) would be a General Monk enhancement tree, that all monks (multi'd or not) get free access to. Put the stances there. But that's kind of boring.
I think the more interesting option would be to create new sets of stances, for each PrE. Henshin gets the current Elemental stances, Shintao gets ones themed around the positive+elemental quasielements, and Ninja Spy gets ones themed around the negative+elemental quasielements. The general "purpose" of each stance would be similar (so Earth, Mineral and Dust would all be the tanking stance, adding to CON), but there'd be variation in how, specifically, they operate. Maybe Mineral is more about percentage bonus HP and healing amp, instead of damage percent mitigation, while Dust provides an incorporeal miss chance, stacking with shadow fade, with a higher percent than Earth's damage percent mitigation (so, better for avoiding physical attacks, but not useful against spells).
He said he was removing the timer. You just pay some more plat. You really think that's onerous?
Frankly, I'm not too sure about removing the timer. It turns things like Savants from a major decision that's supposed to be something you live with long-term, into something you can change on a per-quest basis.
It bears no resemblance to 4E mechanics, at least not any more than PrEs already resemble 4E's Paragon Paths more than they do 3.5's PrCs.