@Bob: In general these affect your ROF more than anything else. However, having more mana also means that you will be able to use mega-spells that lower-mana characters will not be able to. In other words, having a small difference in mana might not make much difference, sure, as you say. But if a spell costs 800 mana to use, and you have only 300, you're not going to be able to use it without major upgrades to yourself. Think Tellah from FF4.
But in seriousness, this gives a choice: use higher-powered/higher-health characters that can only use the smaller spells? Or use a lower-health/lower-base-attack character that can cast the mega-spells that deal more damage inherently. Think Raistlin from Dragonlance.
We just haven't gotten there yet.
In terms of things to adjust your rate of mana recharge, there will be enchants that do that, we just haven't done them yet. So if it's important you to recharge faster, you'll be able to prioritize that in your enchants.
Last point: when it comes to most basic spells, like fireball and such, those essentially ARE mana-free. Anything that costs in the sub-38 mana range is basically "costs no/almost-no" mana range because when you look at your mana recharge rate, by the time you can cast that spell again (1 second later or whatever), the amount of mana you spent from the first casting has already been recharged. So in other words it makes it a spell where you can just hold down the fire button and spam that spell as fast as your cooldown allows, "for free" in terms of mana. Or at worst with the ones in the 36-40 mana range, it takes like half a minute or more of that kind of spamming to get your mana substantially lower. I think it's 34-35 mana range spells that are literally free.
Mana is very much not a holdover from a past system, and goodness knows we're not in reinvention territory on something like this at this time -- that's what the beta phase 3 tag means, to some extent. We're figured out how these subsystems should work, and it's just a matter of implementing the rest of the features and getting them balanced. I think that the above should address all of your complaints, once we've had a chance to actually get it all in (hopefully well prior to 1.0).