I'll be honest and say yes, at least for some people, it's a huge hassle.
The first Pokemon game I really played seriously was Diamond, and I was outraged at first when I learned that some Pokemon could only be evolved via trading, some of my favorites at that! Pretty much all of my DS owning friends didn't play Pokemon, and the wireless router at my place wasn't supported by Nintendo's WiFi connection. I had to go to a friend's house about 20 miles away just to trade over the internet. So, I eventually just bought a brand new DS, since the first one I had was a just a friend's that I bought for like $60. I did all my trading that way.
You may say "just buy a supported router". I could have, but I got the other DS instead, which was worth more to me than another wireless router.
Fast forward seven years later, I bought myself a 3DS, and I can actually connect to Nintendo's WiFi connection on my 3DS~! I should note that I have since changed wireless routers, but they are still unsupported by old DS systems. I guess because the routers are too new? Anyway, it doesn't matter.
So, in short, I say yes trading was a hassle for the fourth and fifth generation of Pokemon. For the upcoming sixth generation of Pokemon, I say it won't be a hassle. The changes to the online functionality of the 3DS, and just the changes that X and Y are making with it's online functions, takes a lot of the hassle out.