Use Only One Pokemon (Trust Me).
Make sure that has a vast movepool, of both powerful special and physical attacks - that cover your weaknesses and deal out great power - supported by a solid in-game Atk and SpAtk stat, that has few or none weaknesses. You could use 2 Pokemon - that cover each other's weaknesses and play separate roles of special sweeping and physical sweeping - and give the more dependent the exp. share.
I did my fastest ever speedrun in a Platinum Nuzlocke with only Empoleon on my team (and HM slaves of course). This may seem a stupid idea but with the right Pokemon for each game you can level up so you are usually 2x the level of any opponent and then just OHKO them and move on. This strategy accounts for weaknesses if you don't have many, you having covering moves and you aren't weak to a lot of the trainer's Pokemon as well as the first 2 gyms.
Trade Pokemon so you receive one that: is of a higher level, has beneficial IVs and EVs, has an over-powered HA (like Gale Wins), has HM moves (so you don't need to obtain them), is over-powered - such as a legendary, works well with the rest of your team but isn't available in the game you are playing.
Know What You Need To Do.
If you know exactly what you need to do in the game then you can plan ahead such as thinking "I need to catch a Pokemon that can learn fly soon because the __ gym is coming up and I need to go to __ afterwards," or something like that...
Glitches can be fun, funny or really useful for completing speedruns such as the walk through walls glitch in some of the Pokemon games.
This is morally wrong.
You can hack a Pokemon game yourself or with Action Replay to give yourself the upper hand such as giving every variation of the PokeBall a 100% catch rate, giving yourself maximum money for EV drinks like Calcium as well as potions etc. or increasing the exp. you get when you win a battle so you level up extremely quickly. You can even go as far as to make your game time become 0 or 1 seconds making you look like an amazingly fast speed-runner (it is so obviously fake people) but if you do that then why pay about £40 on a Pokemon game if you're not going to play it!