At first, Vaati was definitely very difficult. This might have been due to my young age at the time (was probably 10 or 11), but I found myself resetting over and over again, but despite this repeated failure, I didn't find Vaati to be particularly frustrating. My hopes never got down, and it took me about 15 tries to finally get it. I think that the reason that I wasn't discouraged, or had the desire to through my GBA out the window, was that Vaati was a particularly enjoyable fight. The 3 stages added great deal of variety, and I never got bored of doing the same thing. Oh, and as a bonus, the music was pretty sweet. Once I finally beat him, I felt very accomplished, and as with most good games, disappointed that the fun was over.
Since then I have replayed the game a couple of times. The second time through, I believe it took three tries. On the third time through, Vaati was defeated with one try. It comes as no surprise to me that he became easier, because that's how games are in general. Practice makes perfect. If you play a game multiple times, in all likelihood you will get better. But in general, Vaati was more difficult than your average final boss; the only Zelda game boss that took me more tries was the Ganon of LttP. Although, despite the difficulty, Vaati was a very entertaining final boss that takes a long time to get bored of.