Well depending on the crap shoot that is the top loader, you got very noticeable 'jail bars' which is a big annoyance on certain colors/black backgrounds. If you got one where it didn't generate it, or it was so minimal you had to have a TV that exposed it or really hunt for it that was a plus. The top loader if you weren't in jail was a never fail system because it lacked the asinine 10NES chip so games worked or there was something up with your game. Also, no 10NES meant PAL games would run (well like 90% of the unique titles or so.) Preference, the controller is a hell of a lot more comfy, many hands will complain of having a jabby corner digging into a joint as you hold it. That's about it really, and if you loathed the lack of RCA plugs without modification (internal, or using like a radio jack coax to rca box) it was the better system to have.
The old one which is nostalgic and great has that lame lockout chip and that shitty zero insertion force lock on it which jacks up the pins over time making it increasingly more bitchy about loading even the cleanest of games. For years I had to (pre-internet here) consistently clean the games, clean the deck (nes cleaning kit), or push the game in and down, the slide it around a 1/16th of an inch to the left, right, forward, back, some diagonal to get a game going.
As far as any hardware system on a chip clone goes, I'm with you, they suck ass. They all use the same recycled flaky crap flawed setup that puts up a different palette, audio isn't right by a little or a lot by the game (or it's ok), some games just won't work at all (famously MMC5 stuff), usually really badly built and the game pads just suck. The only one worth a crap, and that's still preference is a fully upgraded app/firmware Retron 5 because it'll run anything legal thrown at it really and with the HDMI capabilities for a modern TV.