Just to go with our own development:
Breath of Death VII took us 3 months to make. I'm still shocked we were able to make it so quickly, especially since we had little experience to begin with, but the big thing is we limited everything extensively - NES-inspired graphics, playtime was only 3-5 hours, minimal animation, simple UI, limited number of equipment choices & abilities, etc.
Cthulhu Saves the World took us about 8-9 months to make and then we spent a few extra months on enhancing the game and porting it to PC/Steam. Going in, I thought it would be a super quick job - hey, we did our first game in 3 months so this one should take even less time - but the increased game length, depth (more characters than could fit in the party at once), and improved visuals all acted as different multipliers to the amount of work involved.
Penny Arcade's On the Rain-Slick Precipice of Darkness 3 & 4 - These each took about a year to make. Towards the end of development of the 3rd game, we improved our map creation process to make it easier to make high quality maps quickly which is why the 4th game is so much bigger despite not taking longer to make.
You look at our first four games and see dev times of around a year or less. Then you look at our upcoming RPG, Cosmic Star Heroine, and by the time it comes out (June-Aug 2016), it'll have been about 3 years. Why such a huge increase in development time? There are a lot of factors.
1) Had to largely start from scratch. All of our past games were made with XNA and with each new game, we'd take the engine from our last game and build upon it. However, with Cosmic Star Heroine, we switched over to Unity, both because we wanted to make it easier to go multiplatform and because XNA was discontinued by Microsoft. Not only did we have to rebuild our engine (one which was more sophisticated than our last game) but we had to learn how to use Unity.
2) We wanted the game on a low power system. Sometime mid-development, we decided to test the game out on the Vita which was a system that we really like and had promised to release on. The results were not promising. Crashes due to lack of RAM, frame rates in the single digits, it was a mess. It turns out that the game that we had created that worked okay on my strong gamer PC wasn't very well optimized. Because of this, we had to go back and redo a lot of stuff in order to make things more efficient. Now, the game runs much better on all platforms (flies on the PS4 or a decent PC) and runs quite well on Vita (generally 50-60 fps, good load times, etc.) but it was a lot of extra work.
3) More advanced stuff. We decided to have combat directly on maps which means we needed a lot more frames of animation (most abilities need animation in 4 directions as opposed to just one like you would have in a traditional system) as well as additional code to handle setting up battles and such. Another big addition was our use of Sega CD style cutscenes which meant more art assets, additional code & having to set up each cutscene (they're animated via code like they did with the Lunar games, not just by playing a video file).
4) The game is a lot longer. This wasn't really our intention starting out but Cosmic Star Heroine is approximately twice as long as the longest one of our previous games. More game = more work.
When you combine all this with the fact that we announced the game very early on, it may seem that we've been working on the game for an overly long time, but I hope these explanations make it clear why it's taking so much longer than our past work. And like the article indicated, sometimes you have to interrupt development to focus on something else like the business aspect or marketing.
