I understand your pains. You can find them in Japan a couple of places for MD3 and it will run about 80$ to have it shipped to the US. I recently purchased it after trying to find it on here and KLOV for a few weeks and gave up and purchased it from Hong Kong (English label!! Wee). I find it to be worth the money as it is honestly one of my favourite games on MVS (although I must admit I haven't played MPE).
As far as the MD2 vs MD3 comparison I find these differences. MD3 has better graphics, more characters, and an all new playing mode (Adventure) that is fun. To me it is worth the money definitely, but I find the gameplay between the two very similar. If you just enjoy MD2 as a game to play once in a while, MD3 might not be worth the headache and cost of finding a copy, but if it is one of your favorite games definitely go for it.
Of course if you ever find it for 50$ or less, go ahead
You won't regret it.
Magical Drop fans unite!!!