I believe the 3DO was more forward thinking. The PS3, 360 and Wii are merely 3DO Mk3s. It's basically 3DOs vision of a multimedia entertainment unit come to fruition. Where as the Jaguar was a MegaDrive/SNES on steroids. (of cause 3DO might just be a continuation of the Amiga CDTV and Philips CDi)
3DO embraced party games and casual games more than the Jaguar, (Worms is awesome) although I don't like them, they are a significant genre. The jaguar seemed to pandered to a niche of ex-Amiga and ST users (Of which I'm both.

I believe, thanks to the adoption of CD, in general that 3DO games were more modern too and gave us a better vision of games for the following 15 years. NFS on the 3DO is and was every racing game since. PGR, Grid, GT, Forza owe a nod to a game born from an era when Ridge and Daytona were king. Seminal games like FFVII owe more than just a thankyou to 3DO exclusives like Luciennes Quest and Power Kingdoms. And survival horror games, like D, Hauzer and even Escape from Monster Manor paved the way for Resident Evil and Silent Hill. With that in mind, I believe 3DO heralded in the 32bit/64bit era more than the Jaguar did, and therefore it was better.
The Jaguar, likewise, has no competition for the multimedia epic Wing Commander III. Sure, it's got good space games, but it failed to deliver them in forward thinking way. Rather the Jaguar delivered them in a rather stale last generation way, and in it's games library, the jaguar lacks the number of influential games the 3DO enjoys. Sure the Jag has good games, but very little of it was new or exciting.
I believe a lot of (all be they very very good) Jaguar games are 16 bit (ST, Amiga, Falcon games) on steroids. I think the cartridge, as with the SNES, held the Jaguar platform back. Meaning the 3DO was better in my eyes from a platform basis.
I believe the 3DO had a better collection of 2D fighting games which is still a significant genre. And 3DO was right and better to support them.
I believe, thanks to Japanese/Korean support, 3DO represents a better import experience today. Certainly more enjoyable.
Like I said at the start, I love both platforms, but the fact remains the 3DO was clearly the better machine. Although obscured from gaming history these days, the 3DOs influence on gaming in the past 15 years has been greater than the Jaguars, suggesting that history agrees with me: The 3DO was better.
Having said that, even if the 3DO influenced nothing, the collection of games that it enjoys and the types of games promoted by 3DO, means that it is easier to link back the most modern games consoles to the 3DO (whether they were influenced or not) still meaning that the 3DO was on the right gaming evolutionary path, and therefore, it was better.
The Jaguar was the last flurry in the pre-CD age of games machines. It was the end of the dark ages in gaming and the 3DO represented the age of reason and acceptance.