Hmm, this one is a tricky one.
I was going to say Engineer, since Operatives generally want to be light and agile, and are thus more fragile and less straight combat oriented, meaning Engineers are more likely to be good at both support and combat. However, I wanted to look at what each class could do more closely, and it looks like friendly fire is always on, so spy checking won't be like it is in TF2. Considering Operatives can't cloak, this makes sneaking behind enemy lines to blend in an intriguing experience.
Like most people, I'll play multiple classes, at least at first. But, based on what I've read, the Operative sounds simply epic. Lots of challenge and gameplay variety, it sounds like a fun class to play, with lots of options. As to who is better...well, I haven't played the game, so I can't say for sure, obviously. But it sounds like Operatives try and do their own thing and hang back or blend in, while Engineers have to repair objectives or build turrets, which could make them a target. It all depends on the playstyles of the Operative and Engineer in question, but an assassination oriented Operative could easily take out a stationary Engineer who is repairing or building something.
On the flipside, though, as I said, Engineers are more likely to be tougher, since they don't always need to be as agile, so they could get a weapon and health advantage over the Operative. It all depends on the setting I guess. If the Engineer is on the defensive side, trying to guard something, Operative wins; if the Engineer is the one attacking an objective he might have an advantage, although here he would also be more vulnerable to an Operative sneaking in behind him, since he's moving and can't keep track as well. Basically, if both players were at high skill I think the Operative would win, but at average skills the Engineer would have an advantage, although still not as much as the skilled Operative had.
I could be totally off-base, and I'm not
all that confident with my choice yet, but I've voted Operative for now. It definitely seems like that would be more fun to play. As I said, there looks like there will be plenty of variety. The other classes will all be fun as well, though.
Note: You asked who would
win, and that's what I'm not completely confident about. Who would be more
fun for me, or who I would pick is definitely Operative, though, if I had to choose one.