Hey there Light! Glad to see you drop by. It's cool that you're trying to play at least one game for each region of the main series, and since I think you haven't played G/S/C or HG/SS, you definitely saved the best for last! Gen II is my favorite, bar none. It's the only game to have given you two regions to explore for the price of one, and it's got tons of improvements from its predecessor that you couldn't help but be overwhelmed. Not to mention HG/SS's partner Pokémon feature! I just loved having my Pokémon follow me around just like the Yellow days. I guess I'm just hoping they bring it back some time after X and Y.
I cannot for the life of me remember my fight against Cyrus because it's been so long since I've played Platinum. Or Diamond, for that matter. Still, I think it's alright to use a Master Ball on Dialga given those dire circumstances. I mean I never really use my Master Ball for anything, but the game mascot should always be catched, imo. It's just meant to be that way. :P As for me, I vaguely recall beating Emerald with Gardevoir as the last Pokémon in my party and winning with Calm Mind / Psychic / Thunderbolt / Ice Beam, so there's that for me.
Also, that's an interesting question! I think I'd answer that with Mew. Having Transform that works like it does in the anime (being able to turn into any Pokémon encountered, not just the one in front of you), while still having a pretty cool 'mon to use for battle, teleportation and levitation just beats all Pokémon in every department. I know the numbers that having Magikarp in practically all bodies of water imply, but quality over quantity, imo.
Answering that question was pretty fun! I'll be ending this now, but I hope you're having a great time so far here at PC, Light. Welcome aboard!