I came into Endless Space 2 from Endless Legend. I have not played Endless Space 1.

Playing the game I witnessed already many mechanical and system-wide improvements: 

Political systems are very cool. Manpower is a neat management mechanic. Upgrading systems is given more freedom. Love the different directions I can take in reacting to given quests.

Population Management and Trade routes are way, Bueno...

But I have tried 3 faction so far in Endless Space 2 and with each one I get bored by turn 100+ or so after I complete the faction quest and lose all motivation to continue playing. I'm not loosing, mainly winning...But I just don't have the spark to finish it.

In comparison in Endless Legend despite eventually sticking with Vaulters as my favorite faction to play, I have COMPLETED the game on serious difficulty (Endless just is just too fast for my preferred pace) with Vaulters, Wild Walkers, Broken Lords, Drakken, Roving Clans and think about doing with more.

Its with how despite the fluff and design being much stronger than ever in Endless Space 2, those mechanics feel kinda empty without a core that can develop stories.

I have multiple stories I remember in Endless Legend. Recently my game ended as my Decked out in immune to disease Vaulter Army All named things like "Purifiers", "Gene Marine" or "Curebringer" went up against a massive Necrophage army supported by Titans. This was after being the laughingstock of the Alliance because I turtled up the whole game instead of being wide.

In Endless Space the nature of the universe leaves allot less context for things and a lot fewer things for the imagination to work off of. In Endless Legend If I see a map reveal of a massive enemy faction I see its spiraling Urban sprawls, and monuments. In Endless Space I see big blobs of color.

There is a lack of direction to try or mechanics to be developed. In Endless Space I could develop into naval combat, I may not. I could go Pearl-focused I could not. Focus on a prime species or mix it up with a whole bunch of minor factions. Prepare for Winter or try to rush an early game victory and take advantage of summer. Getting more resources from pearls or from scientific research may yield the same results, but the practice will end up being very diffirent. Focusing on Pearsl for instance means focusing on districts and making much more compact cities. And also is a more limited resource. But its also faster if done right.

Endless Space 2 really lacks many mechanics that you can choose to develop or not. And the ones you do get are generally very similar in terms of benefits. 

Its factions are also allot more samey then Endless Legend. In endless legend, your faction really pushed you in a direction that was really brilliant. The Vaulters for instance my favorites everything about them is so cleverly tied into managing your Tactical Resources, and how this encourages you to go further into science if you want to take advantage of this militarily, really creates a neat gameplay loop, and how you have to manage it in and out of winter. And the Vaulters are the relatively VANILLA faction of Endless Legend.

In Endless Space the Sophons get....Some number bonuses towards science and wants you to research science because you get discounts on them. Your faction quest lends you some further number bonuses.

I dunno If Im missing something point it out to me. I want to like this game allot. Im just...Not so far.

That is extremely subjective and varies on what each person wants or expects from the game. Different people enjoy different settings. I love Endless Legend but I much prefer Endless Space 2 for very similar reasons to yours ironically.
 The Sense of Scale and the identity of each faction is much more fleshed out to me, personally, and I much prefer the impact decisions make in presumably a HUGE ammount of lives and citizens.
 I absolutely disagree with your statement that ES leaves less to the imagination, on the contrary, I can imagine so, so much more when the subject is entire solar systems and civilizations, and unlimited technology potential in comparison to the more primitive medieval societies of EL.

 I honestly believe that all your points are valid, but only in your personal mindset, and ofc there will be people that think like you, theres nothing wrong with that, but I don't believe a single person subjective opinion, be it yours or mine, defines anything of what the game really is.
 To each it's own.