I like the tiers personally, and like it better now its to 10 levels, think its a good balance. A few thoughts I had reading this.
The first issue I see with having gems/potions/ whatnot on every level (other than having level 1000 gems someday) is inventory clutter. You'd end up with tons of slots of different level gems or potions, making both crafting a pain and force you to spend a bunch of time sorting and dropping junk, rolling over to see whats still useful.
Same thought in a way, tiers stop you from feeling you need to spend a lot of time crafting, which might become important once a wider variety of spells come out. You just need to worry every few play sessions rather than every hour or whatnot.
Another issue is that, as is, the tier system helps players that want to have a bit of an easier time and play down from their civ level. Currently if you like to play, say 3 below your civ level, your spells are still full powered from a balance prospective for most of the tier . .and in a way it eases you into playing harder. Gems every level means your spells would be proportional to the low level, but playing back up to your civ level would be a higher barrier. Also you'd always be using underpowered gems compared to civ, and thus be taking a penalty to spell power.
I think part of the slowish start spell crafting wise is that there aren't a ton of spells, but you get enough gems to craft what seems like a lot of the useful ones. Once there's more spells and you need to craft things to account for resistances, you'll need more gems earlier on, which drives you underground faster and thus to killing bosses and leveling, etc.
On an older game with high civ level, its also an interesting choice once you start to get into spells that need rare commodities. There's been a number of times I wonder if I should build that meteor now, and grind that tower . .or wait 4 levels to make it then, or to do a gem run now and try to grab a higher tier even if it'll use a lot of mana and health pots to grab it. Once there's more high tier sort of spells, again think that's going to make the differentiation bigger. I think I'd always "make now" if it was a per-level tier system, and maybe grind more commodity towers as I'd always be ranking up spells.
So I'm pretty strongly for tiers the way things are right now. I could see some of the suggestions to having higher tier stuff have a chance in the upper end of current tier tunnels (especially if you go down more levels in the underground section) - just to discourage gem runs on lowest tier always . . .but to be honest the exp of killing an over leveled pair of bats is so good, I always fight in chunks a few levels higher, and you can level several times just in getting a few gem deposits.
Anyways, that was long, so thanks if you actually read through it all.