One of the main reasons I stopped playing this game was because of the inherit flaw in the game that in most sets, 80% of the cards are not important, not useful, and are just a waste of space. In some sets, perhaps the one mentioned in this thread, it might be 90% of the cards are useless. It does put a bad taste in my mouth when I buy some packs at my local hobby store and not pull enough cards to make the purchase worth it.
It isn't an inherent flaw. It may be standard operating procedure for TCGs, but it isn't an inherent flaw.
And this may be an inherit problem in all TCGs, but I think games like MTG and YGO may not have the problem as much because they don't use an evolution stacking system where the understages play a very little part in the overall game, where the focus is mostly on the highest stage of evolution.
1) Can't speak for Magic, but since they claim "bad" cards have to be released so players appreciate and can hunt for the good cards, I wouldn't be that hopeful. Given their success, perhaps they have a better "ratio" of filler to effective cards. I barely know how to play the game, and am welcome to substantiated input by Magic players.
2a) Yu-Gi-Oh, during the time period I played (release of the game in the U.S. until sometime in 2009; competitive play having stopped a few years earlier) varied, but usually about 10 cards carried a set. Some sets were really bad with not even half-a-dozen worthwhile cards, while others were better. Still even in the best sets, the majority of cards would not be for competitive decks... at least at the time.
2b) Yu-Gi-Oh uses card restrictions instead of set rotation, with cards normally allowed at 3-per-deck, Semi-Limited cards at 2 per deck, Limited cards at 1-per-deck, and Forbidden Cards at 0 per deck. Yu-Gi-Oh also has many "families" of cards built around overarching (and often "named") themes. These two things have helped reduce the amount of filler per set, because often you're getting the newest [insert theme] member. Imagine is SP were still legal, and still getting new cards of support; even less than great support would be significant!
3a) This is very, very important; Prime, you are correct that the focus is on the final Stage of Evolution. This is not actually a flaw in the game. What is flawed is how this focus is executed; lower Stages are simply "filler". If we wanted sets to be more important, lower Stages would actually be designed to contribute to the deck, preferably in a manner that favors their final Stage.
3b) Likewise, pacing is an issue. If we had non-Evolving Basic Pokémon that either weren't strong attackers or took multiple turns to build for any attack of significance and then as I just stated, we make lower Stages worth playing, the trade off becomes non-Evolving Pokémon take less space (usually allowing room for more Trainers) and Evolving Pokémon? Going through Evolution generates advantage like unto running more Trainers.
Look at sets like Team Aqua/Team Magma/SP-related sets, and how many cool mechanics were introduced in sets based around mostly basic Pokemon. Remove the evolutions and suddenly 30%-40% of the set opens up for more options, allowing for cooler combos, which the whole game is about.
The whole game is about making money from a TCG patterned after the Pokémon franchise. Sets should be more than "half good" to be acceptable, so really this game is pretty fortunate that the Pokémon-brand sells it; if this sounds unrealistic I am fine living without TCGs.
Team Aqua Vs Team Magma wasn't viewed that favorably when they debuted, as most fans didn't see those combos outside of specific regions (Japanese players saw them clearly). That was why the first Worlds to feature them was such an upset; IIRC the North American players were trading away most of their Aqua and Magma specific cards thinking them junk, and then the Japanese turned around and won the tournament with them.
As for being focused on Basic Pokémon making that set better... it did have Evolutions. It had some potent (but also specific) shortcuts, but what really helped was the concept of a "theme"; themed cards were allowed to be more powerful, so long as you stayed on theme. When the game shifts to be about Basic Pokémon, I don't enjoy it; I find it "broken", not fun, and as soon as players can test what works, we end up with less options, not more.