R/S/E is better in my opinion for 10 reasons
1. Awesome Music and Battle Music (Notably Rival Music, Legendary Theme, Rival Team Themes)
Music in FR/LG are just rehashed and updated versions if red and green music. No new stuff here.
2. Balanced Starters
Don't get me wrong I LOVE Blastoise and I love Venusaur and Charizard but the Hoenn starters seem more balanced with their mixed type resistances and advantages. For example, Blaziken's mixed type advantage is going to help you in the long run. Fire/Fighting can beat rock and help with ground. Charizard has flying/fire which increases his weaknesses a ton and in the long run doesn't help. If you have a fire pokemon wouldn't you much rather have it beat rock and ground types than beat grass and fighting types that pose no threat?
3. Better Plot
The Plot of RSE is too be more than just a pokemon master and beat rival teams. The plot is about meeting new people and trying new things (Dive for instance, Rematches, PokeSchool that actually teaches something)
4. Better and more legit Professor
I mean come on, Professor Oak says your starter is rare while I see 10 other trainers with bulbusaurs on all the routes.
5. Better Extra Content
Emerald more specifically had the chance to go to the battle frontier, obtain the johto starters and rematch gym leaders, FR/LG had none of these things
6. Challenging
The RSE Elite 4 did not pose a threat, a single Blaziken could tear through the whole elite 4 there. Now although that may be true we can all admit Steven Stone, Champion Steven Stone was much harder than Gary due to the fact in FR/LG you develop techniques to beat and surpass Gary due to him always challenging you.
7. Bigger, Less Crammed
Although Hoenn is mostly filled with water, the game requires you to travel more which is much more fun than getting to the next city easily. Kanto is crammed
8. Two Rival Teams
In RSE there are two rival teams making the story line much more interesting while playing
9. Beautiful Landscape and Maps
Tilesets in RSE without a doubt are cooler than Fr/LG.
10. Secret Bases