I love all of my 1/60´s (desperately waitng till my VE and VT arrive). Like others said I like the proportions of the 1/60´s better:
1. Better canopy and slightly better nosecone (the 1/48 canopy is too bulbous and kinda kills the front view of the fighter)
2. Correct proportions of the arms (the 1/48 upper arms are long and thin)
3. Right size of the tail fins (on the 1/48 the tail fins are on the small side, shorter)
4. All in all the 1/60 has better proportions for it´s three modes.
5. I like the VF 1A and VF 1J heads more than the 1/48. On the other side I must say that the VF 1S head of the 1/48 puts the 1/60 head to shame, and the seamline doesn´t bother me at all.
6. It´s gonna be the most complete line (waiting for the Q-Rau and Monster)
Making the 1/48 justice:
1. It´s a better put togheter/finished toy, barely noticeable seamlines, smooth sculpt with lot of detail (air brake, removable engine covers, highly detailed landing gears and landing doors)
2. Perfect transformation (nothing has to be removed, not even the heatshield).
3. Better connecting hardpoints for the weapons.
4. The Fast Packs are incredible, no words to decribe them (all the detail and features put into them), they´re also the right size (the 1/60´s are on the small side).
Proportion wise I like how the 1/60 looks against the 1/48. In fighter mode with the "fast packs attached" the 1/48 looks better than the 1/60 (however the 1/60 like I said has better nosecone and canpy).
Owing the two scales is a win-win situation IMHO.