Pre-emptive TL;DR: The way species work at the moment makes it painful to use specialised species/robots. This seriously hurts xenophile ethics, machine empires, and anyone who goes Genetic Ascension. We need more automation and fine-grained control to make them actually useful (and fun).
If you have a planet with different species, you immediately run into several problems:
You need to manually drag every pop around the planet to make sure they're working appropriate tiles. You can only stop paying attention when the planet is completely full. If you don't happen to get the species in the proportions you need, too bad.
Your leader pool immediately starts filling up with a new species, and inevitably, the species turns out to be Fleeting and Slow Learners. Unless they're a completely foreign species, there is no way to prevent specialised prole-pops from entering the leader pool.
Straight away, this is so annoying that it's not worth seeking out Intelligent species for labs, etc. At best, it's tedious busywork, and at worst it actively hurts your empire. This is clearly not ideal.
The problem gets even worse when you try to specialise pops. You can only modify whole planets, so each planet must be dedicated to mineral production, research, etc; but if you then settle a colony, migration causes a mishmash of species. You can make a leader caste, but they won't show up as leader unless your empire is dominated by their unproductive pops. As a result, genetic modification is a pain in the ass.
But each of these issues is pretty easily solved by changes to the existing systems:
Planets should check their pops and tiles, and automatically optimise production (unless the player takes manual control). The AI already does this, and so do sectors; there's no reason it shouldn't work for core planets as well. Aside from allowing species to slot in seamlessly with the existing population, it would also mean people might stop resorting to Caste Systems just because it's less annoying than full Slavery.
However, alien pops rarely migrate to my planets, often because they're already completely full. To make multispecies empires actually possible, planets need to be able to draw from a more generic pool of available migrants; for example, if I have a migration treaty with the Clever Space Dragons, we shouldn't necessarily need an entire pop to migrate over. It should be possible for my planets to start growing a CSD pop from the smaller numbers of migrants trickling in. Moreover, it should be possible for the planet to open up room for that new pop, if necessary, by getting a native pop to leave or converting it into an invisible "idle" pop.
And suddenly opening your borders makes you more productive and flexible, if you have the right ethics, rather than just making you regret starting a game.
To make sure you don't get flooded with terrible leader species, the game has to determine which species are good. This is actually pretty easy, at least in concept; take a persistent pool of 10 candidates, and each year they gain XP, grow older, etc according to their personal and species traits. The best candidates (according to their level and positive/negative trait count) get shown to the player as potential leaders.
This automatically culls poor leader species (Slow Learners and Fleeting will tend to be lower-level) and promotes good ones. It also ensures the player has a choice of many leaders, if they wait for the pool to choose a new slate of candidates, and eliminates the late-game problem of "well my 7-star admiral just died, looks like I'm hiring a 1-star, there goes 20,000 fleet power."
This system is also easily tweaked. Authoritarians could ban poor leaders from the pool, further increasing their average leader quality. Pairing this with genetic modification, you could draw every leader from a single specially-designed species. Fanatic Materialists could have an expanded Scientist candidate pool, leading to more intense competition and more reliably strong scientists.
And again, aliens and subspecies become a really cool and powerful option for those with the ethics to use them.