We're slowly working through updating our late 90s house- I feel your pain OP, it's a lot of work and requires a lot of creative thinking! My feeling is with a 90s house you're fighting three main issues; the lack of high ceilings, the lack of good light because the windows tend to be on the smallish side, and the lack of period features (which goes hand in hand with all the cheap, synthetic materials they seemed to love in the 90s!)
Things that have helped include: using any optical illusion you can that makes the ceilings feel higher, such as replacing the coving with a more slimline version; fitting unobtrusive, close to the ceiling light fittings; hanging curtains closer to the ceiling; and replacing curtains with floor to ceiling ones (I've even moved radiators so I can put in floor to ceiling curtains, honestly it makes such a difference!)
To counteract for the lack of good light make sure all curtains/blinds sit well clear of the window, either completely above if you're using blinds, or completely to the sides if you're using curtains. You want to let in as much light as possible, and you don't want any part of your window obstructed with window dressings. Fit a mahoosive mirror either opposite or on a wall perpendicular to the window; honestly, go way bigger than you think you need. You want to bounce as much natural light around as possible.
Regarding the lack of period features I don't think you can reverse engineer those in, for me it would look a bit twee. You could however, fit an amazing contemporary fireplace, which would give focus to a room. I've also found using quality, natural materials to replace the cheapie 90s ones really seems to help- proper oak for example, to replace the orange pine. Or proper marble 'penny' tiles rather than the weird porcelain mosaic tiles they seemed so in love with then! I also found it helps if you add lots of 'texture' to compensate for the lack of period details; natural linens, seagrass wallpaper, chunky knitted throws, and oak flooring would all help- if you look at new build showhomes you'll see developers use this trick all the time! Its why showhome beds always have about 15 cushions and 3 throws on them!
In a similar vein I also found putting some really soft planting around the outside of the house seems to 'soften' its 90s brickwork- blousy roses and hydrangeas for example. It sounds like it would be incongruous, but it really does seem to help.
Next on my hit list is to replace all the flimsy, hollow MDF doors and their shiny fake brass handles with solid oak ones and proper brass handles; and to replace the orange pine handrail up the stairs with a proper oak one... Small things, but they all seem to add up.
I've ended up finding inspiration is some quite weird places! Look on Rightmove at how developers style new build houses. Also the Perfect Stays website has been great- its a high end holiday lettings company in Cornwall, but their properties tend to be fairly modern with a really relaxing vibe. I've stolen loads of ideas from there! It's also been quite inspiring to look on Pinterest at American beach houses; all clean lines, natural fabrics, soothing colours, but all very decidedly 20th century! Good luck!