What are the differences of anime in 1990s and 2000s in terms of technology used? What are the main differences between anime in the 90s and in 2000s in terms of technology used (like on twos, on threes, etc)?
This is a fairly tough question to answer, as most changes did not just apply to Anime, but to how movies, series and even advertisements as a whole, and the way they got made. 

It is however an interesting time period you picked, considering the economic slump of the 90's, which they only started to recover from in 92


  A slump in advertising revenue, dwindling birthrates, and the popularity of alternative forms of entertainment like video games and cell phones have led to sluggish prime time ratings and a decline in the number of anime since the peak in 2006... ...The Japanese anime industry is at a turning point. - Nippon, 2013


Rise of 3D animation and CGI

All though 3D animation was already existent around the 1940's. It had a 'said' breakout year in 1991. As more and more studios started to adapt the technology, we can slowly see it replace older, more Traditional Animation techniques throughout the 90's and during the beginning of the millenia.

Due to these changes, there where also significant advances in the field. Such as the 2000 breakthrough in capturing the reflectance field over the human face, being the final breakthrough to making digital look-a-likes of actors, Or the 2001 Motion capture, photorealism, and uncanny valley.

The later of which was applied on the 2001 Japanese-American Final Fantasy: The Spirits Within, which was the first photorealistic computer-animated feature film and remains the most expensive video game-inspired film of all time.

Besides obtaining a first in Photorealistic computer animation, Japan can also claim the title for being the first in using cel-shaded animation, with Appleseed.


  "innovative use of out-of-the-box animation software to create Hollywood-style effects at a tiny fraction of Hollywood budgets."
  Mark Schilling, The Japanese times &amp; Toshio Suzuki president Studio Ghibli


Death of traditional animation

Traditional Animation, also known as hand drawn animations, or cel animation.

During the 90's as more and more studios started to adapt digitalized animation, the art of traditional animation started to slowly die out. Some studios dived straight into the deep, leaving traditional animation behind almost immediately, while others started by mixing the digital and traditional ways. 

This would continue till FujiFilm, one of the major cel production companies, announced they would stop cel production, leading to a industry panic, hastening the switch to digital processes

Around the early 2000s most studios left behind traditional animation for the more modern, digital animation. 

There was however 1 exception to this, Sazae-san. But even though it was the sole survivor, they also gave in to the modern age in 2013. When even they said goodbye to cel animation.


  "It's the culture of Japan. We want to continue making the paints even if that cuts into our profits." 
  Taiyō Shikisai head Shigeji Kitamura 


http://www.nippon.com/en/features/h00043/ 

begin 90's turning point facial animation
Historically speaking, the first SIGGRAPH tutorials on State of the art in Facial Animation in 1989 and 1990 proved to be a turning point in the field by bringing together and consolidating multiple research elements and sparked interest among a number of researchers
https://en.wikipedia.org/wiki/Computer_animation