Definitely Hoenn starters for me. First of all, Venusaur vs Sceptile. I think Sceptile is better. While Sceptile is fragile as hell, it is very fast and has a good movepool. Venusaur lacks a good grass move in 3rd gen (apart from Solarbeam), Sceptile gets both Leaf Blade and Giga Drain as level up moves (it has to stay in Treecko form until lvl 46 for Giga Drain though). Sceptile also gets False Swipe, Thunderpunch, Dragon Claw, Crunch, and several other offensive moves so has much more coverage. Venusaurs Sludge Bomb just lacks in coverage.
Charizard vs Blaziken is tricky. Blaziken has better attack and Sp.Atk stats but Charizard gets better speed. They both get good coverage moves, stat boosting moves, and good STAB moves. I think they're fairly tied, although Charizards immunity to Earthquake is really useful (although it pays for it an electric weakness, which is often fatal for it as everything carries Thunderbolt).
Blastoise vs Swampert is easily won by Swampert. There isn't really anything that Blastoise can do that Swampert can't also do (except spinning I guess). Both get Counter and Mirror Coat, both get Hydro Pump, Ice Beam, Earthquake, and so on, but Swampert has a large edge in the secondary Ground typing that grants it Electric immunity and a rock resistance. Extra STAB on Earthquake also helps tremendously against Metagross, and in alround stats it is very reliable.
Master balls are the cheapest thing ever invented. It's more fun catching everything with balls that can fail. 'caught Latios in the wild without master ball ftw'