The way I see it, ascension paths are meant to be just that, a way for your species as a whole to try and reach the next level of existence. Basically the people of your empire go through the growth pains of trying to 'evolve' themselves ultimately through some means. Psionics believe they can reach perfection through the mind, gene-therapists believe they can become perfect through body, and synths believe replacing the body entirely will give them perfection. It's possible to mix and match and realistically I would see any society trying all three as well as alternatives such as megastructures or world shaping but ultimately only one can truly win out.
Now bear in mind this is more of a fluff response than a game response. If you reach enlightenment, your mind becomes one with the universe and you eventually become a being of pure energy and don't need a body. If your body is able to adapt to anything, immune to everything and doesn't need anything, then you can do anything. Same for machines because if you can just replace your body with parts that do whatever you need for you, then the universe is yours to play with. However, if your body is perfect, then why replace it, and if your cybernetics can do anything, then why have a body to begin with. Ultimately it's pointless to do multiple paths once one of the three wins over. Not to mention that if your people are perfect, then you now have all the time in the universe to experiment, build mega structures and so on because nothing can stop you.
Reversely, not perfecting your people means you're still trapped to the confines of the universe. Each dyson sphere you build, every ring world you make, every planet you terraform is just another means to try and prolong your race and keep them going. In a sense, not picking an ascension path and following through to the end is what makes you a fallen empire. You've reached the pinnacle of your people's ability to research and learn but don't know how to move on beyond taking more space up, which in turn means more resources dedicated to keeping your people going.
Obviously as far as the game is concerned, you're not going to turn into energy beings or become so flawless your people become as one or the galaxy is one giant dyson sphere that you use to travel the cosmos because you'd have long since won by then... There are a bunch of abilities you can take besides ascension that, like others have said, are just as good and still represent a critical moment in your people's history. Just because you don't chose any ascension perks in your playthrough doesn't mean your people won't eventually settle on one, it just means they had other things to deal with first.
I'm sure the devs are aware of this and will be adding more stuff as time goes on to fill in each and every little gap the game currently or may have down the line.
And if not, mods!