Part of it was military adventurism (coup plotters among the military) -- why arm them when they would just use the hardware against the government? Part of it was the 1997 Asian financial crisis, which we had a more difficult time to recover from than our neighbors. Part of it is as Nihonjin1051 mentioned -- a breakdown in our relationship with the US. There was also a resurgence in separatism and rebellion that dictated increased funding for our ground army at the expense of the other services.
There was a spate of ship decommissionings in the 90s (around 8 frigates, I believe), because there was an expectation that we were going to get new ones soon, but the financial crisis put a kibosh on that, along with the plan to get F/A-18s to replace our F-8s and F-5s. We lost the F-8s to a volcano eruption, but they were in disuse before that -- it began to get difficult to source spare parts from the US to keep them flying (kicking them out of the bases could have had a hand in that). Much like the F-8s, although we 'retired' the F-5s in 2004, we actually stopped using them long before that.
Kicking the US out of the bases was actually a long, drawn-out process, and it came down to a narrow vote in the Senate. The votes weren't based on any lofty ideals of nationalism or loyalty/hate of America or anything like that, but rather just base opportunism by the politicians involved. The US had helped the ruling government quell a coup attempt, so some opposition senators that had supported the coup retaliated by voting to kick the US out.
But the US is now back in, the coups are a thing of the past, the economy is growing again, and we just made peace with the largest rebel movement. I'm optimistic about our near future