What day and time of day are you arriving?
I have had a few passages through the new Quito airport (although not for a connecting flight), and transiting passport control and baggage each time was pretty quick, less than 30 minutes. The airport is not that big in size or in volume - it ranks in the range of say, PIT or CVG/CMH. So 90 minutes should be more than enough.
However, its geographic location can make for some difficult landing conditions. One of our flights made 4 separate attempts before diverting to Guayaquil for about 90 minutes until wind conditions subsided and then we landed at UIO.
So if that connection is super important you might want to give yourself much more time in case one of your flights are delayed or some other irrop happens.