Think about it, it does makes sense. Forcing a player to think: "Well, I'll just fire off this last Arcfire while my opponent is dead" isn't really great game design (in my opinion).
In other words, forcing someone to manage their inventory and think tactically.
I'm sorry, but "should I fire off this shot and set the tome to recharge while I have this gap in the action, or do I assume that I'll get attacked as soon as the other player spawns in, and to hold onto my tomes" is a way more interesting strategic choice than "well, I KO'd someone, so my spell is going to regenerate".
You're kind of just splitting hairs with this one. I would assume the poster's "one charge" means two shots, not one shot. The example would remain the same with simply "two shots" remaining.
The poster specifically stated having one charge only giving access to half of Robin's recovery. That is not going to be the case. Even with only one charge remaining, you'd have access to full recovery. You just wouldn't be able to recover again for a few seconds after it breaks.
A regeneration time would still require you to tactically manage your tomes, merely in a different way, and it would, as you said, make misuse significantly more punishing. Thirty seconds would be far too much under any circumstance.
It turns it from a "manage inventory", akin to what we actually get in
Fire Emblem, to a manage time mechanic. It becomes all about rationing attacks compared to overall time, rather than rationing attacks with regards to usage remaining.
With a "4 shots left" mechanic, it all becomes about how you use those four shots. You won't want to use specials carelessly, because you only have so many left, then you're vulnerable.
Regenerating flat out actively
encourages using specials blindly. Rationing them would be sub-optimal. "Well, I'm full on charges, I might as well try for this shot, it'll regenerate again anyway". Like almost every game with recharge timer mechanics, you are always better using the ability instantly, because anything else is downtime that is wasted. Any time you're full is time the ability is spent not recharging, which is wasted time overall.
Let's say you have five shots total before breakage.
If durability loss is permanent until breakage (which I believe it is), you have to ration each of those shots, make each one count.
If durability regenerates every five seconds, you will be firing an extra shot every five seconds, regardless of the situation, because there is no reason not to.
Rationing shots and determining when to use it with a constant regeneration would only ever become an issue if you had to spam a single attack constantly. It removes the entire "breakage" or "tactical use of ability" concept entirely, and makes it basically nothing but an anti-spam feature.
For break>replace, I would imagine the time won't be more than 5~7 seconds.
For regenerate/break>replace, I would imagine 1-2 seconds per charge, and 7~8 seconds for the full recharge. Anything more than that is getting ridiculous.
One to two seconds a charge is completely ridiculous already. At that point, it doesn't even become an issue. Heck, the spells seem to have a longer cast/finishing lag than that.