I thought Dr Doom was fine... the appearance of other villains was what kept me very interested...
And that episode with Hulk was cool...
Dr. Doom, IMO, showed up too often and was often foiled too easily. Within a 26 episode series, he showed up 8 times; on average of once every 3-4 episodes. He seemed to always be portrayed not as the greatest threat ever, but a typical super villain who there was never any doubt he would be foiled and shaking his fist at the heroes by the end credits. It didn't help when he was involved in some formula plots like a "mind swap" plot early on. I know that the intention was to homage the Stan Lee/Jack Kirby era, where Dr. Doom did do things like shoot the Baxtor Building into space or do mind-swaps, but the problem is that Dr. Doom should be Darth Vader; hell, he was the INSPIRATION for Darth Vader. He should be awe inspiring, not trucked out and beaten every other episode like he was Dr. Claw. It probably did help that not even Ben Grimm tended to take Doom seriously, but considering how often he lost, it was hard to take him seriously. That's not to say every Doom episode was bad, but some were too formulaic and it would have been better if he was treated more like Magneto is, built up and used sparingly, but when he is used, it is a big deal. And a show can only go so far when it botches the arch-nemesis. THE BATMAN was perhaps destined for mediocrity when it botched the Joker.
That said, FF:WGH did handle many of the villains who weren't Dr. Doom well. I thought they succeeded in making the Puppet Master very creepy (and look, they only used him twice, but each time was a big, epic deal and he was treated as a mega-serious threat; with Dr. Doom it was just, "Oh, here we go with the Doombots again, whatta revoltin' development"). I liked how Super-Skrull was built up over several episodes. Since I watched the show around when SECRET INVASION was heating up, I found the comedic angle to the Skrulls refreshing. Ronan the Accuser was a bit one-note, but I guess he often was until ANNIHILATION. And the Mole Man, who unlike Doom usually should be treated as a joke, was often very funny.
To me, the last 13 episodes were better than the first 13. I think after the first half of the show, the writers got onto a better comedic flow and decided to focus on that and the character banter, since they were better at that than the straight up hero stuff. Which was good; episodes like "CONTEST OF CHAMPIONS", "THE CURE", and especially "SCAVENGER HUNT" were hilarious and entertaining. By and large, though, was despite the fact that a lot of the action scenes were ho-hum and average, the Four themselves were handled well. I though Reed was written with a lot of wit; instead of being a straight man, his genius was utilized for functionality as well as laughs (his elastic body actually made for some decent sight gags). Ben was his usual self, but I liked how he wanted to be cured, he wasn't overly angst ridden and brooding about it all the time. Johnny was sometimes hit or miss; his voice actor put in a lot of energy, and when he was on, it was funny. The downside is sometimes Johnny went too far, and came off as a fop or a schtick instead of a character. Sue was more consistent, although more of an attempt was made to have her be more assertive from the start (aside for the one moment where she faints, but that was only episode 3, so I can forgive it). She did fall into too many "Ugh, can't hold it!" kind of moments like Jean Grey always tends to, but she's usually the most "normal" one to get the Four in line. The episodes that had the most heart were often the ones that seemed to start off with a focus on comedy.
The show was also very self aware with it's comedy; in "BAIT AND SWITCH", Reed is doing an experiment on some broccoli and Ben quips, "I'm going to end up fighting this, aren't I?" Naturally, he does. And yet while that episode had a lot of fun with the Four swapping powers (ironically, a plot that the second film used a lot), the heart was there when Reed was determined to keep the rock form so Ben could be "more human" with elastic powers. And of course "CONTEST OF CHAMPIONS" had that "Thing never gives up" moment.
In conclusion, I don't think that show was the best ever. I probably do find it more enjoyable than any Fan Four show that was on TV or film so far, and it is a bit under-appreciated. Cartoon Network did it no favors, either. And even the sheer timing of being the first new superhero team show after JLU ended probably worked against it, and made expectations absurdly high.