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I tried to make use of most of the pokemon that I found interesting, but to begin with I kept pokemon based on the effort it took to acquire them. After the 2nd gen I gave up on the legendaries because I didn't find them interesting any longer. In gens 3 and 4 I hadn't much interest like the first two. My interest wasn't sparked again until 5th when I decided I wanted to really do it all again, but this last gen got me pumped enough to collect them all.
Still, each of those selected have their own special place for me. They really represent my favorite pokemon or took a lot of effort to get, but I used them all for a time for sure.