Well,
1) there is not any, AFAIK, singleplayer skirmish. Dawn of War isn't just about an awesomely fun campaign and good multiplayer. It's also about being able to battle it out against any race you want, without the possible humiliation that MP griefers will heap upon you.
2) a cover mechanic that doesn't feel very Warhammer 40,000-ey. I thought the cover mechanic of the original DoW was awesome and fit very well within the milieu of WH40K. After all, a large crater is the perfect place to sit in and fire from, as opposed to open ground.
3) the cover system of Dawn of War "2" is more akin to something from a WW2 strategy game, or a FPS game. The need for almost excessive micromanagement in cover-rich environments with lots of rounds flying all over the place isn't something I care for.
4) the singleplayer campaign of Dawn of War 2 centers fully around the Blood Ravens. It doesn't reference any other race as an ally. Granted, vanilla DoW1's campaign was all about the Blood Ravens, but there were occassions where you fought with some Imperial Guard troops and tanks under your control, which was pretty cool.
5) Dawn of War 2 simply, IMO, lacks the scale, depth, and span of the original series up to Dark Crusade (SS was at most okay). The campaign of DoW2 (judging from the demo, as I don't own DoW2 and have no plans on it) is semi-meta-map based, but is much more centered around objectives and leveling-up your sergeants and FC.
6) going back to the lack of scale, I doubt that DoW2 has some of the truly massive maps of the original (though even 8P maps that are enormous can become a little crowded; this is solved by either making 8P-sized maps as 3-6 players, or by simply closing some slots).
7) from all appearances, DoW2 seems very StarCraft-esque in regards to the amount of micro needed. DoW1 is surprisingly light on micro with few exceptions (these being certain commanders, the Eldar, and special situations like dancing ranged troops away from CC units).
EDIT: I forgot this- I will give DoW2 this though- they have 'Nids and they have pretty good graphics. But I actually prefer the more "obsolete" graphics of DoW1. Mostly because it will run smoother on my comp (the DoW2 demo would slow down pretty severely at times; DoW1/WA rarely slows down on me).