It’s not an EU project, but there are EU countries involved in the funding, which means EU tender regulations apply.

Wendelstein is cheaper, but according to wikipedia it also went over budget. “[…] while the total cost for the IPP site in Greifswald including investment plus operating costs (personnel and material resources) amounted to €1.06 billion for that 18-year period. This exceeded the original budget estimate, mainly because the initial development phase was longer than expected, doubling the personnel costs.” (The original source is a dead link, but you could probably find something corroborating fairly easily.)

I’m not saying ITER is a bad project, I don’t even think the cost is a problem, I just think that the regulations surrounding the financing of these kinds of projects often do more harm than good.