I think they just wanted varietyThis is what happens when all you desire is to be as close of nature as possible but your friend says "hey, you should try out that new Colosseum thing!".
On another note, Breloom is the odd one out, since it's based on fungal life rather than animal life (animals that are usually bred, at that). It's not like they would run of out candidates in Gen I-III, so I wonder why?
Like you have:
-fish (the fancy fish)
-some mushrooms for flavor
And you don't use Tropius (for fruit) because the joke is the pokemon as a whole, not what they produce
e: Checking the grass types available for this their options were pretty limited. You could only grab Pokemon in RS or Johto pokemon and in terms of "pokemon based on something actively edible and not just producing something edible" its really just Breloom and Seedot. Everything else is just A Plant or makes food you can just pick off. If Exeggutor were available they might've used that instead. Maybe could've used Sunflora, but I think thatw as earlier in the tower and you can't pass up some fugu!