Some thoughts in no particular order for you or other readers...I have only had the Vado SL since June but can relate.
I bought the non EQ because (a) the non EQ was already the most expensive bike that I had ever purchased and (b) I didn't see the sense in having fenders on the bike. At that time I was completely unaware of the differing drivetrain and gears....of the FutureShock etc. I did observe that they put a more street oriented tire on the EQ bike. I didn't fully understand that the rear rack was integrated with the fenders. In my case it seemed that I knew far more about the Vado SL when compared to my salesman.....but that is another story. Back in June the non EQ 4.0 was on a steep discount at $2499US so I jumped at it. I'm glad I did.
I'm not a kid anymore either and I didn't/don't plan on riding in the rain. I have, however, been caught in heavy rains more than once. I still didn't miss having the fenders....I'd have been soaked either way. It happens.
This is all a learning process and I was up for the challenge. This forum helped me to become more knowledgeable, however, I was still a 'babe in the woods' at my time of purchase. There are things that I just hadn't realized prior and I will definitely be a more educated consumer should I purchase another bike in the future.
I added flat pedals, grips with horns, and a RedShift suspension stem to the bike (and re-routed my headlamp due to the stem replacement). That is all that I have done and I am 98% happy with the bike as it is.
I don't miss fenders whatsoever and the inclusion of fenders prevented me from the ability to utilize a platform car rack safely/soundly although I now know that there are ways to overcome this. Though subjective I also prefer the naked look of a bike without fenders....that's just a 'me' thing. The rear light on the non EQ prevents me from easily installing a dropper post, however, I have found the OEM seat to be quite comfortable...and with the suspension stem added I no longer feel a strong need for the dropper post. I like that rear seat-light functionality and I do not wish to delete it.....I feel safer with it as-is.
I would have appreciated a Spesh OEM rear rack solution for the Non EQ Vado SL. As discussed, without the rear fender the OEM rack requires a top mount solution. There are of course solutions to this but none have yet jumped out at me as the right solution for my needs. As colder weather is upon us I now, for the first time, really feel that a rear rack could be useful to me. The bike is darn close to perfect for me...and I realize that any new bike will require some add-on bits and customizations as us riders are all different.
All in all.....especially given my naivety at the time of purchase.....I am quite pleased with my Vado SL 4.0.
FutureShock is nice - if you can choose a model with it. When I last looked it was just the Vado SL 5.0 models, though looking at the 5.0 EQ the specs don't list it but the photo shows it... Would want to confirm in person. Other models you can use somethign like Redshift as you've done.
Fenders are good for commuters who may need to ride on wet pavement after a rain, or for folks in wet climates who experience more wet pavement than dry. For those who can pick and choose when we ride, something like the SKS X-Blade temporary rear fender can work well for those infrequent times we want a rear fender.
Lights - integrated is convenient but hate that none of them blink. Personally I want it to blink during the daytime (DRL), and at night I want something brighter, so I'm already using an aftermarket light. For the rear, I use a Varia RTL515 light/radar so the non-blinking integrated light is also superfluous.
Rear rack - it's unfortunate SBC chose not to provide rack stay mounting bosses, but aftermarket solutions exist such as this mount which attaches to the seatpost. You can then skip having a rear fender serving as the rack stay and gain a wider choice of racks. Or go with a quick release option allowing you to easily switch from rack to no rack: Ortlieb Quick Rack
Dropper post - note this is different than a suspension seat post. Intended to let you lower your center of gravity and move around a bit more on the more technical downhills you might find in gravel or singletrack riding.