To begin, I want to make it clear that I recognize that we all have differing play styles and we will all see things a little differently and therefore the ideal situation is to be able to change EVERYTHING.
Your first question confuses me a bit and it might help for you to reiterate it. If you mean to suggest that a recharge will fail very often with enchant at level 65, then I believe you are mistaken. I have not done my own testing, but, from what I've looked at so far, it would seem that at 65 recharge becomes consistently successful and comparable in success rates to the other skills such as conjuration. The only thing that might appear to be a failure is getting those annoying 1s on the random roll but we'll get to that in a second.
Carrying, for example, a large stash of common soul gems around could prove to become an issue but I'm not inclined to believe that this should be a real problem since, on the whole, I think it's overkill to be able to constantly recharge your artifacts as you deplete them. This is about how easy you want the game to be and, again, we all have different preferences.
Now, about those annoying 1s. Correct me if I'm wrong, and I may well be, but I think a Golden Saint is 300 points? Well, if that is the case, then you should be seeing an average return of something like 112.5 which is much more reasonable than a lousy 3 points. Certainly, even with high skills, we may miss with our swords but we can still be relatively competent and eventually slay whatever we are whacking away at. I am more interested in what the average numbers look like in this case. Of course, since I haven't looked into these numbers at much depth, I could be just plain wrong about this so please correct me in that case.
Soul gems are not really difficult to locate. At least this is the case if you are using Tribunal. In just plain Morrowind, I think that you might only be able to find restocking gems up to common so beyond that you would need to mod something in and no one would blame you if you did. I don't really see 12lbs of rocks in my inventory an issue if it means that many more uses of my Jinkblade. And about the Amulet of Shadows... it's already overpowered as it is, in my opinion. 5 charges of 80pts chameleon for 60s seems like plenty to me. But again, it's preferences. Also, there are plenty of mods out there that make the game "difficult" enough to warrant having access to more useful tools than vanilla offers.
I think that people not using recharge is more about it not truly being necessary in vanilla due to the auto-recharge factor. Just rest for x number of hours and presto. Removing that factor makes recharge much more attractive for players. I realize that recharge is probably intended to be an attractive choice unmodded, and, honestly, I think it is if you are not going to exploit resting all over the bloody place. In certain areas, being able to instantly recharge your Amulet of Shadows without resting could prove to be extremely valuable and well worth carrying the extra rocks around.
As far as I can see, without difficulty-enhancing mods, the numbers look relatively okay. I think that to make them much more in the players favour would be a bit unbalancing. For this player, at least.
edit:
I should probably add that there being a "punishment" for higher skill levels just seems odd.
My first question is a bit.. obscure, I guess. What I was trying to say is that in almost any other skill, success equals success in a boolean fashion. A successful "Open" spell does not half open the door, a scamp is not half summoned, a lockpick does not reduce the lock 10 or 20% at a time for each successful attempt. It works or it doesn't, simple as that.
If all you are going to do half of the time is recharge an item a small amount, then it is a fail, and that is as simple as that.
A Golden Saint is actually 400... but remember that the formula is:
x = (enchantTerm + intelligenceTerm + luckTerm) * fatigueTerm
roll 100, success if roll < x
on success restore charge: soulgem charge * (roll / x)
So, by the example I gave
x = (100 +20 + 4) * 1.25 (if not fatigued) or x = 155
If the roll happens to equal 1 then
soulgem charge * (1 / 155) or 400 * 0.00645 = 2.58 Round it off you get 3.
If x = say 70, then in reality any roll above 70 is an automatic fail, so the average successful roll will work out to be around 35, so:
restore charge = soulgem charge * (35 / 70 ) or 200 in the case of a golden saint. That's not so bad, but again consider the case of that Amulet of Shadows with a capacity of 1200. Six grand soul gems with golden Saint souls to fully recharge it. What's their value these days? 7000 gold each, I think... How much does it cost you each time you miss with your sword?
Just resting to recharge is fine, assuming you can. How often have you found yourself in a bad place but at a relatively peaceful spot and tried to rest only to get "You can't rest here, enemies are nearby.". do you really want to just stand around in that particular spot waiting for your item to recharge? I guess it wouldn't be so bad if you had something to read, and a mod that makes time pass while you do it.
Recharging all of your items on the fly is not really the question here, but I doubt that you could do it in any case. I'm not looking for a cheat, just a more realistic solution. People don't use the recharge function because it so loaded against them that it's not worth it. I just want to change that a little bit.