Depends on the type of music you play, Overall, I find PRS designs among the better but some find them sterile. Also the crazy flame top designs can be super expensive and many find them over the top. That said, the bridge, pickups, and tuners are all examples of better designs than the big three. Wrap around bridges for example, hold tune better, are easier to setup and intonate, and are easier on the strings than the traditional stop tail style. Locking tuners are a big advance also.

Instead of brands because those are often tied up with the look of an instrument, I'd recommend you look at the individual components. Locking tuners, wrap around bridge or floyd rose (not a cheap knock version), coil splitting or active pickups or other pickup advancements.

I'm a couple years removed from playing so this might be out of date but I really liked the PRS SE line, the mid-pro level Jackson line, and some of the mid-priced G&L line (Leo Fender's second company and set of designs). I tended to play blues and metal so my selections really fit that style.

Oh for acoustic, I really like the Blueridge guitars and Seagull guitars. Seagull are made in Canada with pretty great materials and designs but much cheaper than most American made instruments.

I'm more of a high end custom guy for acoustics, in my experience you get what you pay for MUCH more on acoustics. If an electric plays well, you can make up a lot of sound from the amp (tube or modeling if you need variety), good pedals, and aftermarket pickups. Acoustics sound great when you play them or not. I always tell people to spend on the Acoustic and balance it out with electric.