There's really not a huge statistical difference between he and Manuel from an overall standpoint. Given that they have a similar number of attempts, you can make a decent direct comparison.
Orton: 124 attempts, 85 completions (68.5%), 890 yards, 5 TD, 3 INT, 7.2 YPA, 10.5 YPC, 13 sacks.
Manuel: 131 attempts, 76 completions (58.0%) 832 yards, 5 TD, 3 INT, 6.4 YPA, 11.0 YPC, 7 sacks
Point production is pretty similar, 19.75 with Manuel, 18.7 with Orton.
That largely agrees with what I've seen. There's not a huge overall difference, except for one. Orton makes plays late in games that EJ doesn't and that's why he's on the field instead.