Yes, but it is still not clear to me how increasing PC baseline effectiveness by adding powers that are regained after a short rest is any different from increasing PC baseline effectiveness through gaining levels or magic items. In all cases, you need to increase the baseline difficulty of the monsters encountered if you want a challenging fight.
Complexity is a separate issue and (IMO) one that can be managed. One could argue that the real issue with respect to complexity is not so much the rate at which the powers are regained as it is the number of them.
Okay, discounting complexity. The issue with encounter-based design for characters is that it forces encounter based design on DMs. Yeah, I keep repeating that and trying examples, so I'm going to try a different tactic by comparing apples and oranges. Yeah, I'm doing it.
You can plant one of two trees in your garden to give you fruit - an apple tree or an orange tree. If you plant an apple tree, it's going to give you 5 apples at the end of every month but the apples won't go bad for a month. Meanwhile, the orange tree is going to give you 1 orange at the end of every week, but the orange will go bad at the end of the week.
In both cases, you can eat one fruit per week, either eating the orange as it drops or by saving your apples and only eating one per week. What you can't do though is use more than 1 orange at a time - it's going to go bad before you get another one. So if you get really hungry, you can eat all five apples at once and just not have any fruit until the end of the month. But if you get really hungry, you still only have that one orange to eat.
Now you have an evil squirrel. The squirrel sneaks in and gobbles up one piece of fruit at the end of the week. If you planted the orange tree, it's not a big deal - that orange was about to go bad anyway. You just get a new orange the next day, whoop-dee-doo. But if you planted the apple tree, it's now a big deal. You had 5 apples but now you have 4. At the end of the next week, you're down to 3. That evil squirrel is slowly taking away all your apples and if you were saving them up for the end of the month because you knew you might be very hungry then, that's a big deal.
That's what the resource difference is like. I have no idea if that analogy makes a damn bit of sense, but I'm running low on ways to explain it. If you have an encounter-based design where
the majority of the abilities that the characters have recharge at the end of a short rest, then any encounter that in and of itself doesn't challenge them is a waste.
There's no tension because any resources they expend they will get back at the end of the encounter. There's no difficulty because they can expend those resources to do more damage or be more accurate. There's actually no point whatsoever to the encounter because it doesn't affect the game in any meaningful way, it just eats up time. You're better off just telling the players "You killed a couple of goblins standing out front and got 75XP each" and saving yourself a bunch of time. The players winning the encounter without expending any meaningful resources that will impact the rest of the adventure is so statistically likely that it makes having the encounter in the first place a waste of time and energy. In order for an encounter to have any meaning whatsoever, the players have to be challenged in each and every encounter, putting them at risk of dying or forcing them to use what few daily resources they have. Any encounter that doesn't do that isn't worth running.
He's dead! Everybody's dead! Everybody is dead, Dave!
If you still don't get it, run the following scenario in both Pathfinder and 4e with a group of first level characters - same number of characters (at least 3 and up to 5) of the same general types (try to match classes/roles when possible) in each. "Your guide has finally led you to the goblin caves, but he starts acting twitchy and nervous, glancing to a large rock 20 feet across and 20 feet high. Your Sense Motive check is successful and you realize he's set you up! Your Perception check indicates you notice the poisoned dagger he's tried to secretly slip into his hand! You're still out of sight of the caves, so you might have a chance to save this if you act now! Roll initiative." The enemy in this case should be a non-minion non-solo of Level 2 in both cases, preferably something with a lot of dexterity and finesse but lower AC and HP, a skirmisher in 4e and a PC-race rogue in Pathfinder. If you don't have Pathfinder, 3.5 or 3rd works just as well.
That is almost exactly the set-up when I realized how pointless it is to try to have "small" encounters in 4e compared to Pathfinder/3.5/3rd/2nd/1st/etc. The only difference is that the PCs were level 3 and the enemy was a Level 4 Doppelganger. The fight was entirely pointless because the PCs had far too many resources they could throw at the enemy without worrying about losing them. They could throw their encounter powers (doing more damage and/or being more accurate) without having to worry about needing them later because immediately after, they could take a short rest and get them all back. The doppelganger didn't stand a chance, and after two turns I just stopped the whole thing and told them they won without even finishing combat.
I believe I am now officially out of ways to explain this concept. If you still can't get it, please say so and maybe someone else will have a way to explain it that will make more sense for you.