Here would be some things I would do:
Lisbon: 3 days
Milan: 1 day – 0
Pisa: only needs 1 day
Athens: maybe skip because you’re not going to any islands that athens would be an access point to. Corfu to Thessaloniki would save a lot of time as opposed to skipping down to Athens, which many people are dissapointed with. Maybe try to see Meteora instead in inland Greece.
Istanbul: 4 days
Careful Travel times between these places: Istanbul – Budapest – Vienna will be really long, I would try to fit some things in Bulgaria or Romania in.
Try Bern instead of Zurich, or even better the Lauterbrunnen Valley.
Munich: 3 days
Berlin: you’d appreciate 4 days in this city i think, there is so much to learn, experience.
Hamburg: Don’t bother, I was so disappointed with this city, really a dud.
Forget Groningen and Lille too in favor of places in Bulgaria, Greece, Romania.
Hope this helps.

Thanks a lot for the feedback, tigrouflip! It definitely helps a lot. Hmm.. I think I will take out Hamburg then and reconsider Zurich. I don’t think I’ll be able to make a stop at Bulgaria or Romania because I need to get a visa for each country to make a visit. It sucks to be Indonesian, traveling-wise. As for Groningen, I’ll be visiting a friend there (and probably stay at his house too) so I think I’ll keep it. Will take out Lille though to save me a couple days. Meteora seems amazing. Maybe I should go there.

That’s because Athens is a lot like Los Angeles…there’s no obvious large concentration of sights and districts (the historic center is definitely worth a visit but is relatively small), but rather amazing pockets spread over a large area, and [if you know which districts to go to] amazing nightlife. The average Let’s Go backpacker doesn’t experience this side of Athens, and many of the “disappointments” are also outdated opinions from before the city started undergoing a massive make-over, which is on-going (yes, despite the fiscal crisis). But given the OP’s time contraints…

I second this advice. I would add a day to Corfu, make it 3 full days in Corfu, maybe a day in Ioánnina, a day in Metéora-Kalambaka (definitely worthwhile), then Thessaloniki for a couple days (I think this is a great city), and then on to Turkey. If you have more time, check out the Zagoria region from Ioánnina.

This would be an awesome Greece itinerary.

Thanks for the feedback, luv_the_beach! Yes, I think I’ll try that.

i agree Pisa is not worht more than a few hrs, see the tower, move on, milan also not worth more than one night, better spent in other spots in italy Rome especially. On your list munich, Rome, prague are all brilliant more time the better, try cesky krumlov a few hrs from prague for a night or 2. overall full on trip and you will probably need to chill out at some point for a few days. Amsterdam also brilliant to see (do the heinkein brewery tour)