Hi - how are these versions different to the official 3D Sega Ages ones? Ta
The 3D version is a port by M2 that has some QoL stuff. Dunno what exactly but I know Sonic 1 has spindash. These decomps are Christian Whitehead's recreations done his own engine with a lot more content. You can read the Retro pages for the differences.
Sonic the Hedgehog (2013 game) (sonicretro.org) Sonic the Hedgehog 2 (2013) (sonicretro.org)Sonic the Hedgehog CD (2011) (sonicretro.org)
The decomps allow more flexibility. Sharp, pixel-perfect display. Remappable buttons, scripts for advanced mods, devmenu. Recently it was updated to support SDL 1.2 which is why the 3DS port runs great and we will soon have a mod loader later.
As for the 3DS port, it's a bit rough. Could use some more optimizations. Even on New 3DS, All 3 games lag on Special Stages but it's still playable. Sonic 2 takes it like a champ. When the game frame dips, audio will never crackle so it's not as bad as rough emulation. The only audio hiccup is in Sonic CD where it takes a sec for the track to switch after Time Traveling. Very minor
Hope that answers your question!