No. Minish Cap is nowhere near the best 2D Zelda. Now, granted it was really good for such a short game, but it isn't quite as good as A Link to the Past. And by "isn't quite," I mean the only possible way to beat ALttP is to be a 3D console game.
Now, Minish Cap had many positive points that have started to affect the rest of the series.
+ Instead of the item being built for the dungeon boss, the dungeon itself is built around the use of that item. A large example of an impact would be Arbiter's Grounds, where the rails for the Spinner were EVERYWHERE.
+ Many items were used again in the final battle, one way or another, rather than being useless once you stepped into the warp space. So far, this has yet to be reimplemented.
+ Made excellent use of the "Origin" Story and pushed the GBA SP to its limit.
But it definitely had its drawbacks.
+ It was too short. Six dungeons, with a few faux-dungeons, and I, while never using the Pegasus shoes as needed, was able to beat the game in a mere 3 hours. WALKING EVERYWHERE!
+ One of the Heart Pieces forced you to waste several hours of gameplay searching for shells just to create figurines.
+ There's really nothing you can do once you've gotten the Mirror Shield and you already have everything. No minigames, no nothing.
ALttP on the other hand... Pros,
+ Influenced every "major" Zelda game to date, whether it be in terms of plot, or the usual "Hijacked by Ganon" plot twist.
+ Longest of any Zelda game, and yet, in the proper hands (like my own), it is able to be beaten in just over 2 hours.
+ This Link is the most powerful of any Link in any game. He has a very great supply of weapons and utilities that the other Links do not have.
Cons,
+ For the newer gamers, it's too damn difficult.
+ Once you start to get the game, it no longer is a challenge.
Overall, ALttP is much much better than TMC, but that is my opinion.