The difference between the per-encounter and per-day resources, IMHO, in this situation are as follows. Every encounter in a per-day model is "significant" because the total effect they have upon a character must always be considered. In other words even casting a low-level spell must be considered against whether that spell may be useful, or even necessary in the next encounter or the third or fourth. This makes every encounter significant in the fact that it carries consequences that must be accounted for besides what is best right here and rigt now.
In a per-encounter model, the only concern in using one's abilities is what is effective in the here and now. You need not consider, as long as you use only per-encounter or at-will abilities...what the ramifications of holding in reserve or unleashing full blast will cause. Instead it makes sense to always unleash since they will come back. In other words there is no consideration for long term consequences only short term.
I think of it like this...
Per-day abilities are more like chess in that a move you made 15 minutes ago will affect your capabilities later in the game...in fact all the way to the end.
Per-encounter abilities are like a fighting game(Tekken or Soul Calibur) they take strategy at the moment of the combat, but if you make bad decisions in the first round and loose, you still start at full power in the next round(though there are certain games where loosing the first round causes you to start with less life in the next round, and IMHO, it's a superior style of play.)
The other difference I see is that with a game that promotes long-term strategy, you have time to recognize the mistakes you've made and adjust your strategy to those mistakes outside of combat. In confining strategy to the moment of combat, it does tend to promote a live or die(just like the fighting game) type of encounter.
Okay a few problems I see with your example...the sending wave after wave without letting them recover per-encounter abilities. This is not the same as the per-day abilities resource management(it's not just about attrition). You've in effect taken the characters from 100% capacity and stuck them in a fight at 20% capacity...This means that at this point they use their per-day abilities, and if they are enough...they survive. If not they die. The player's didn't manage their resources over a long period of time(Unless they are aware there will be more fights in the same "encounter"), you surprised them with an encounter and the resources they have left is based on random factors(how hard the earlier fight was, if they were throwing abilities for "fun", how dangerous the second fight will be, etc.). Basically it's promoting one playstyle and then doing the switcheroo on your players without warning. It's more likely to get them killed than to promote any type of long-term considerations.
To take the fighting videogame example above...it would be like playing that and one player being aware that depending on how much you use your abilities affects your power level and life in the next round, but the other player doesn't. I guarantee player 1 and player 2 are going to approach that first combat in totally different ways. And my money would be on player 2.
I don't get the more "dynamic" encounter argument. In D&D 3e you can do the same thing and with a finer grain of accuracy. An encounter can again be challenging in and of itself without the risk of death or even major depletion of resources because the management of the resources itself is dynamic. It gives a raneg of resource depletion that the DM can use to shape how long the PC's can go on, which IMHO is a good thing since the DM is the one who must be prepared for the encounters they will experience. Only got 2 to 3 hours for play well then have three major encounters, each of which should deplete 30% of the characters resources. Got 6hrs to play make up 4 encounters that deplete 10% of their resources each, then one balanced for 20% of their resources and a Big Bad who takes 30%. I'm not seeing how these are any less dynamic than the per-encounter abilities.