Problem for The Matrix is it wasn’t even the best “what if reality is an illusion” in that period. Dark City is much better in all ways, and Thirteen Floor had a better structure but lacked the budget to really make the story work.
Often times if you want to find truly great movie you need to look beyond the blockbuster. Go to the art house, or flops (that are often really good but lack the ingredients for mass appeal, Drive is a great example of that, truly an excellent movie, but also not the movie they advertised and never should have been a wide release).
Oh yes. Dark City was all kinds of fantastic. Lost that DVD in a move. Really need to hit Ebay.