An archer typically won't hit a wall that they are using for cover either, but may well hit a wall that their target is using for cover. The problem arises when things are moving quickly which isn't really modelled well in a turn-taking system... Another option is to assume that if you miss by four or less then the cover made the difference and should therefore be subject to the attack, but if you do that then it punishes near-misses more than obscene-misses...
Removing the concept of completely exhausting your spells is significant and should not be taken lightly. A 16th level caster in that system could cast fireball all day and scorching ray for the rest of the week, this removes the great disadvantage of high-level casters which is that they can't do anything without expending limited resources. If you want to kill a fighter then you throw a single tough encounter at them, if you want to kill a caster then you summon stuff to attack them at 2 hour intervals for a week, eventually they will be trying to fight off a dozen raging celestial badgers with a rusty knife... Record the footage from your scrying device and sell it to the fighters guild... Note also that anything free can be used constantly, A cleric can wear an amulet of wisdom and cast bear's endurance on themselves once every 5 minutes, healing becomes a non-issue with unlimited cure minor wounds, a caster with a wand of lesser restoration can cure themselves of exhaustion and keep casting top-level spells for as long as they have charges and roll 20s on their saves, this may cost a lot of time to be done in combat, but it could be used in conjunction with summoning spells and such to cause no end of grief...
The whole thing is very incongruous with the D20 system. It has a table which needs to be looked up, the vast majority if tables in D20 follow simple mathematical rules so the whole thing does not need to be memorised. The system references the ability score instead of the ability bonus, this is extremely odd. I do not see how the table is generated and therefore do not know how to generate a table for different classes, such as rangers and bards... If it followed a more consistent system, such as one based upon halving the cost every four levels(cantrips would, as usual, be treated as half a spell...) 8, 7, 6, 5, 4, 4, 3, 3, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 0... but that wouldn't satisfy the system because the system is completely arbitrary... And lets not forget that basing spell-casting directly on the ability score makes it even more important than it was before. At 20th level you would have 10 spell points from levels, you almost certainly 'start' with more than that from your ability score, it will likely take you until about level 100 for class levels(not caster levels for some reason...) to be as relevant to spells per day as your ability score.
At 1st level a wizard with 18 intelligence gets 2 magic missiles and 3 acid splashes, with the mana system they would have 2 magic missiles and 1 acid splash, 1 magic missile and 3 acid splashes, or 6 acid splashes, so the notoriously brief 1st level wizard has even fewer spells...
Unlimited availability of true strike, invisibility, cure wounds, shield, grease, empowered ray of enfeeblement, any summoning spell, would all be ridiculous, a level 19 wizard could use extended summon monster II to flood an entire dungeon with celestial badgers. The shield spell would become permanent at level 15. At level 8 detect magic becomes permanent outside of combat and literally EVERYTHING is a light-source up to and including the paladin's cod-piece and all those random pebbles on the ground that were picked up by the gelatinous cube that has been following the party...