As much as I loved Generation 3, there were several MAJOR flaws that made them extremely difficult to finish (and I mean completely, not just by beating the E4 and Champion).
For starters, Feebas was almost impossible to catch. In fact, I never seen it once in any of the Gen III. The major flaw in the capture method was that you could ONLY find Feebas in one of six random locations that were supposedly dependent on the Trendy Phrase you created at the Dewford Town community center. Furthermore, these six locations were supposed to vary daily, meaning that you could fish for hours in several different spots and NEVER catch a Feebas. I don't know if anyone else encountered this issue, but it was extremely annoying to me, so I just gave up.
Next, Mirage Island was virtually inaccessible. I know this place existed in the games, but in order to get to it, you had to do a bunch of number crunching to figure out what Pokémon you had to show to the one elderly gentleman just to coax it into view. However, even figuring what Pokémon he needed to see one day, it would automatically change the next. Because of this, I never was able to get to Mirage Island (and, now, I know I can't since the internal batteries in each of my RSE games died a while ago. They still play/save, but day-to-day events no longer occur).
Lastly, the 3rd Gen games carried over the old Physical/Special attack format that was still divided into types and not the kind of moves that attacks actually were. While it was still okay at the time, I found it rather annoying having to memorize what attack types fell into what category, and it got even more annoying trying to remember which moves counted as direct attacks and which ones counted as indirect attacks (if anyone remembers, that was necessary in order for certain abilities to work and, to an extent, it still is).