I love both villains in their own may, but I personally like Thawne just a wee bit more.

Don't get me wrong, Syndrome is funny and has cool weaponry (plus he's more realistic for not having any superpowers) but Thawne actually has a tragic backstory. Sure Syndrome got rejected by his idol, but Thawne's family treated him like crap and his quest for the Flash's love was all in vain after he discovered that he was basically destined to become the Scarlet Speedster's greatest enemy instead. If only he had support and better mental health, everything would be okay.

I also love C. Thomas Howell's performance in The Flashpoint Paradox.