I would actually go with Gengar over Alakazam. Alakazam has the superior Special Attack, but it only gets a grand total of six non-STAB special moves -- four of which are from breeding. This essentially forces you to use Psychic, Thief, and Shock Wave, plus one other random move, and Shock Wave and Thief aren't even very good. You could use Calm Mind in the last slot to make it terrifying, but the fact remains it only gets one good special move. Seismic Toss is an option, but that's not always the most useful useful, as it does a fixed amount of damage.
Gengar, while it doesn't get to utilize its superior attacking stat on its STAB, instead gets a wider range of special coverage moves, which is arguably more useful. It gets Giga Drain, Thunderbolt, and Psychic, plus Dream Eater + Hypnosis if you so choose to perform that strategy. The type overlap with Venusaur doesn't matter, not in an in-game playthrough -- it may in fact be good, as Venusaur can use Poison moves that Gengar cannot.
So I would recommend Gengar, because while it doesn't get to use either of its STABs well, neither are really useful (Poison is only good against Erika and you have your other team members to help against Agatha). It gets wider coverage than Alakazam, which I believe is better than only being able to use one STAB move well.
Hope I helped!