If you want to see what a real rip-off looks like, take a gander at the sort of stuff Zynga has done.
Back in the days when I was playing Facebook games--Lord knows why--I was a regular Farm Town player. I remember being stunned when Farmville came out and I gave it a spin...the initial release was a complete, unabashed, gratuitously flagrant copy of Farm Town.
As has already been pointed out in this thread, Greenheart took Game Dev Story as an inspiration (and it can't be stressed enough that the free and open and gracious acknowledgement of this inspiration is part of what sets Greenheart miles apart from the likes of Zynga). They then ran with it in their own direction, designing something that is very much their own game.
I've logged a lot of hours playing Kairosoft titles, and they have a consistent feel, style, and gameplay emphasis that are all quite different from what Greenheart has created. If you set the shared theme to the side for a moment, you should be able to see that in all other respects Game Dev Story has more in common with its Kairo stablemates than it has with Game Dev Tycoon. While for its own part, in actual gameplay Game Dev Tycoon has more in common with Velocigames' Gamebiz 1 and 2 than it has with Game Dev Story.
(I haven't played Gamebiz 3...the pricing seemed too ambitious to me and I wasn't sure the third entry would be different enough from the first two. But maybe other folks here have played it and would recommend it? How about other titles in the same vein? I love this sort of simulation, but the only other computer game with this theme that I can remember trying was the unfortunate German import Game Tycoon.)
All that said, I do see two missteps that Greenheart made that helped foster the "rip-off" meme. The first was the choice of title. If I were their lawyer, I would have strongly recommended that they choose a name less reminiscent of the Kairosoft's title; if they ignored my advice, I would have fully expected to receive a nastygram from Kairosoft's lawyers. (Do note, however, that the essence of the legal complaint would not be that the two games were the same thing...but rather that the choice of name might cause consumers to wrongly believe that the two games were the same thing.)
The second misstep was the decision to copy Kairosoft's distinctive calendar/clock display so precisely. (If I were on the design team, I'd have pushed for a more turn-based approach anyway. Not that I'd have any business being on a design team...I don't think my prior experience in playing around with lo-res mode on an Apple II would be that much of an asset.)