Completely disregarding sales for a moment, which do you think was actually the better system, and why?

I enjoyed the Vita more than the 3DS for its niche Japanese titles. Library wise, the 3DS was indeed superior. Though I only ever used it for the handheld Zelda games.

Spec wise, the Vita was also a beast for its time.  Killzone Mercenaries was jaw dropping for the era, and not thought possible on a dedicated handheld.

On the principle of which has the better Tales of game, the 3DS.

VITA easily. Hands down. Without question. I'm not a fan of the 3DS. Vita is like the SEGA Saturn of handhelds. It's so full of great hidden gems. From Uppers. Macross Delta. Soldner X. A ton of RPGs, Action games that are console quality. Of course, there is also Persona 4 G and Gravity Rush. Thankfully the RPGs don't have that fucking hideous Chibi shit 3DS games have. A lot of Mecha games on Vita as well. 3DS sure it had SMT IV and DQVII on it but for the most part, 3DS was such a boring, lame system for me.

VITA is still a class-looking system. Wonderful screen. Dual analog. The only real downside was yes the memory cards. That's the one area 3DS wins. There is not a day where I'd choose 3DS over Vita.

3ds cause a lot of vita games, I can play else where but quite a lot of 3ds games I can only play on the 3ds. The hardware on the Vita is better though. Also Fuck the memory cards on the vita. Super nonsense is what that BS was.

Not to mention playing Senran Kagura in 3d mode was fap worthy

3DS is so underrated.

Well, let's see.
I'm biased towards the 3DS. I've had a 3DS since launch, and put well over 1000 hours into it (New Leaf alone is my most-played game of all-time with 600 hours played). But I finally got a Vita earlier this year.
3DS gets the edge in: First-party games. number of third-party exclusives, lower price, DS backwards compatibility, non-propriety memory cards
PS Vita gets the edge in: Technical specs, third-party games that I actually want to play, two analog sticks
I think both are underrated. A lot of people see 3DS as B-tier and Vita as C-tier. I would put 3DS as A-tier, and Vita as B-tier. I have to overall pick the 3DS for Nintendo games like Animal Crossing: New Leaf and Fire Emblem: Awakening.
The future is the Vita for me though as I haven't had it for long. My 3DS still works but has a damaged hinge. Honestly, I might have to get a used 2DS or New 2DS XL if I ever plan long-term to use my 3DS again.

There are only a few games I really like on the 3DS, but then I look at the Vita and it has like...nothing.

From a hardware standpoint, definitely the Vita. It just feels like a more premium product. From the OLED screen to the capacitive touch screen. I'd argue that, in some ways, it feels more premium than the Switch.

Game wise...3DS just has more overall quality games than Vita. So...I choose 3DS

If you take library into account, 3DS wins easily.