6870 Ultegra Di2 Upgrade

I have an older Cervelo S5 (2013 or 2014?) with the old external battery. Thinking about upgrading with a new internal battery, junction box, wireless unit, and shifters (probably $800 total with used shifters, labor and cables).

I get:
Di2 stats on Garmin
More aero battery setup?
Buttons on my brifters?
Renewed battery
Probably optionality on bar-end shifters for my clip-ons Enve bars

Worth it or just put it towards a new road bike? (Prices don’t really make me inclined to want to upgrade though).

I have the same set you are wanting on bike and its a great a great all rounder with clip ons and drops with Di2.
The Ultegra R8050 series will let you program how you want the shifting, via Synchro or non-Synchro. I prefer the later, preference in the choice of when the front shifts, not the system’s programing to do it for me.
I think
The STIs are more comfy and and have a better shift click plus you have 3 buttons on them if you have a Garmin as you noted.
I’d recommend getting the RX805 rear derailleur just because it has a clutch and you can go up to a 34t no issues. It’ll let you have a larger ratio in the rear without worrying about the chain slack if you ride rougher roads.
Can probably get the whole setup for 1100, the switches with cost the most because they can still be used with a 12sp setup.
And you can plug the system into the charger unlike the other.

I would upgrade the lot to 12 speed Ultegra/105 mix to future proof it for a while.

Can probably get the whole setup for 1100, the switches with cost the most because they can still be used with a 12sp setup.

Switches are (potentially) really inexpensive with this generation as you can use a simple momentary switch. No need for the “smart” satellite shifters used in the current generation.