So this discussion popped up in #oi and I thought it would make for an interesting topic of discussion. From what I can tell the two frontrunners are GSC Abra and BW Archen so I'll do a quick write-up. While "strongest" is a bit of a vague category it probably doesn't mean stuff like the box legendaries who usually come too late to be of any significant use.
Abra
Abra's most notable downside is that it's difficult to catch and comes with no moves for a few levels (as is standard for Abra throughout the series). However, as Goldenrod has both the Coin Case (which means you can just buy an Abra if you can't catch one) and has the elemental punches as TMs, this is an extremely trivial downside.
Abra evolves at Lv. 16, giving you a Pokémon with base 120 Sp. Atk, 105 Speed and extremely good coverage. It does require trading to fully evolve but if trading is not an option Kadabra is extremely powerful as is.
Archen
Archen's downsides are that it involves backtracking to obtain (Relic Castle -> Nacrene City, which isn't terrible as you will have the bike by this point) and its ability which cuts its offenses in half when it's at half HP. As you will have both plenty of healing items and money by this stage this is another trivial downside (especially as Archen OHKOs damn near everything anyway so it probably won't get hit). Archen also has a good movepool.
Anything that Archen didn't OHKO before, Archeops will. It is amazingly powerful (base 140 Attack, 112 Sp. Atk and 110 Speed) and the worst thing that can be said about it is that it looks really stupid in 3D.
There are other extremely powerful Pokémon that I haven't covered here, such as BW2 Magnemite and XY Riolu/Lucario. As DHR will chew me out if I don't mention this I highly recommend looking at the in-game tier lists as they'll usually be a good place to start, along with your own personal experiences.

Abra
Abra's most notable downside is that it's difficult to catch and comes with no moves for a few levels (as is standard for Abra throughout the series). However, as Goldenrod has both the Coin Case (which means you can just buy an Abra if you can't catch one) and has the elemental punches as TMs, this is an extremely trivial downside.
Abra evolves at Lv. 16, giving you a Pokémon with base 120 Sp. Atk, 105 Speed and extremely good coverage. It does require trading to fully evolve but if trading is not an option Kadabra is extremely powerful as is.

Archen
Archen's downsides are that it involves backtracking to obtain (Relic Castle -> Nacrene City, which isn't terrible as you will have the bike by this point) and its ability which cuts its offenses in half when it's at half HP. As you will have both plenty of healing items and money by this stage this is another trivial downside (especially as Archen OHKOs damn near everything anyway so it probably won't get hit). Archen also has a good movepool.
Anything that Archen didn't OHKO before, Archeops will. It is amazingly powerful (base 140 Attack, 112 Sp. Atk and 110 Speed) and the worst thing that can be said about it is that it looks really stupid in 3D.
There are other extremely powerful Pokémon that I haven't covered here, such as BW2 Magnemite and XY Riolu/Lucario. As DHR will chew me out if I don't mention this I highly recommend looking at the in-game tier lists as they'll usually be a good place to start, along with your own personal experiences.