In my opinion ROTS has been one of the highest overall quality lines that Hasbro's put together since the modern line's inception. What Saga was in 2002 could be considered practically a knock-off toy line in quality compared to the ROTS line in 2005. They literally are like night and day, and I think the overall quality we have seen in 2005 if one of a list of major contributors to a successful toy line.
The fact is that Star Wars competes for the almighty dollar at retail like every other toy in the aisle with it, and Hasbro's perhaps learned that sub-par figures dominating a line will yield sub-par results in sales at retail. Couple that with a well-received film critically and I think Star Wars had a good set-up this year for success, and it was a nice thing to see.
Hasbro's key changes were hiding action features, making sure figures were generally more neutral and poseable, and trying to key in on those character selections everyone could generally be pleased with. I mean, they saw the fact that two Clones could and ultimately did sell very well, and both these Clones were aimed at unique demographics. Pretty cool really from a collector's point of view and it was just the better for us that both were fairly good figures from our (general) POV as well.
Hasbro had 2 unique Anakin's, 2 unique Obi-Wan's, 2 unique Yoda's... That's an interesting method of attacking retail really.
Anyway, that doesn't mean that, for ROTS's level of quality with some figures compared to others, that there weren't stinkers in the mix. Popular sellers, maybe just because so little was available at times, but even the stinker figures have sold in many instances.
Some of the worst of the ROTS line to me though are:
-1 & 2 Anakin & Obi-Wan... Weak sculpts and in my opinion some lack of accessories (saber-hands are cool but they need to include a saber and open hand as well) hurt these two greatly. Good for kids perhaps, but the kids in my life want my Evolutions Anakin and begged for Pilot Obi-Wan when they saw mine so you be the judge.

-Grievous' Guard... I actually don't MIND this figure too terribly, it suits a purpose, but at the same time I look at it and it would've been a great figure to super articulate. I'm not sure how "off" the head is in its size but it does look odd. A cloth cape and heavy on articulation would have easily swayed any negative thoughts I had but sadly we got none of that.
-Battledroids (SBD or BD)... Weak plastic. It's excuseless in the modern line, and Hasbro has got to remedy the Separatist situation. We need droids, and we need them now, and we need them able to stand on their own at all times. Hasbro has to wisen up on this.
-Mace Windu... What the hell is up with his head and arms? Not Hasbro's best sculpt, and not to mention how loose and unattractive his arms are. Mace is a figure that should've had a "Pilot Obi-Wan" kind of figure later in the line. THAT would've made one hell of a great figure.
-Obi-Wan Jedi Kick... I got this figure for my gf's oldest son's birthday, and he despised it. I took it from him and promised him the Pilot Obi-Wan that had just come out, and fortunately found them in time for both the boys' birthdays. The figure's sculpt is attrocious, and his action feature (though hidden) is obtrusive and barely works if it works at all. Terrible quality, and much more of a Saga figure than a ROTS figure.
-Wookiee Warrior... While it's kind of like the Grievous Guard in that I don't totally despise it, the posed legs, and lacking articulation are major drawbacks on this figure, and they make it pale in comparison to its preview counterpart. I think had Hasbro just articulated the knees and not pre-posed the feet, I'd have been pretty much 100% happy with him as-is. He's really kinda neat, just flawed enough to make you annoyed with him.

-Cmdr. Bacara... What the hell is Hasbro thinking!? You have a perfectly good Commander sculpt. You have a #6 Clone sculpt that's great. You've proven you can do this figure justice with articulation and a feature, so why don't you just do this Hasbro? Sadly Bacara fell well short of anyone's expectatons and he was the Clone's redheaded stepchild. Bacara also proved what a lower quality figure does... It sits at retail, while his not-even-in-the-film-counterpart Red Commander has sold out consistantly all year. I see a problem here, and Hasbro should too. Hopefully Bacara's crapitude isn't repeated with future Clones.
-Destroyer Droid... Come on... The E1 figure's superior to this, and they put this figure out early enough that they could have re-sculpted the head for the E1 figure and really made fans happy. Instead we got the Saga pegwarmer re-issued to us.

-Commander Gree... A figure Hasbro should have just left till another day when they could have given him his due. His sculpt's horrible for the character (great for a regular Clone though), and his paintjob is equally inaccurate for Cmdr. Gree. Hasbro should have put out a SA Utapau Grunt, THAT would have made people really happy... Or even a SA Shocktrooper would have been more well received than Gree. I mean, he's one of the only easily obtainable "Final 12". Doesn't that say something about the quality?
-Vader's Med Droid... While not a pegwarmer in my area, he still sucked in that he had the same cheap plastic the BD's had. If the falling over was a feature intended by Hasbro, I'd maybe be more lenient, but man this figure bites. It topples like Vader's throwing a tantrum in your collection room.
-Capt. Antilles... Taking the Bail figure's basically identical outfit (more or less) and taking away most of the articulation is a recipe for a piss poor effort on Hasbro's part. You gotta make Antilles equally cool to Bail Organa's figure, no excuse. Sculpt's great, articulation horrible, and in my world articulation always is slightly more important than overall sculpt... Still, if he was completely inaccurate he'd still suck even if he was SA.
-Utapau Warrior... Cool, but I'm finding mine fall over. That alone is really disappointing. Excuseless too so I'm gonna give some negative opinion here on him irregardless of how cool he is in sculpt and such.
-Zet Jukassa... Another weaker effort, and in this same COl. 2 line. Zet's articulation is the weakest of any of the secondary Jedi figures in ROTS. For a kid who kicked more ass on screen than any minor Jedi, he should have had a really nicely articulated figure.
-Yoda Spinning Attack... A modern line turd if I ever saw one, this figure is just attrocious looking head to toe. If I had to, I'd probably label this the worst of the ROTS line just off the top of my head, and compared to these others. Yes, Yoda spinning attack reigns supreme for suckitude.
I'm sure I could pick apart a lot of other figures but I wanted to get a quick listing of my least favorites together... Others aren't so much bad as they have annoying flaws. Tarfful for instance lacks knee articulation and a good paintjob. The Neimoidian Warrior's lack of knee articulation but has ball/socket joints... Those are so-so figures that are neat to have but could have really been a lot higher quality.
And the Deluxe line... Ugh. Pretty much the entire first wave except the Anakin to Darth Vader figure sucked, and that Anakin wasn't high on my list. I think Kicking Obi-Wan and the Emperor were the worst, but as per usual the Deluxe line underwhelmed a bit. I thought Stass Allie was ok, I thought the Spider Droid was a marked improvement, and I thought that the Crab Droid was cool but could've used some better sculpting to make it more realistic... Not glowing reviews but passable. I'd even say the Clone Jettrooper is sorta cool, and the Yoda w/can-cel was neat really... Vader w/Med Table was probably the best, but really the Deluxe line never makes your eyes pop out of your skull unless it's in a non-movie year...
I mean, compare ROTS's Deluxes to stuff like the Hoth Wampa. I'd take the Wampa.
Anyway, ROTS was a pretty cool line to me, and I was pretty well happy with 90% of the Collection 2 figures overall. Even the pegwarmers like Bail, Palpy, and Mothma are still GOOD figures. They're just dull as watching paint dry, but they get good marks from me. The Jedi rocked, it was like one big apology from Hasbro and I liked that. Very cool, and ROTS dished out some greats...

Even the list of figures I made that were bad, most of them would probably have been god-sends in the Saga '02 line had they been there. I'd have killed for any neutral posed Jedi even if they had an action feature and a bad sculpt.