Just some quick math here.
For ease of math there will be a few assumptions made.
- Both the Rogue and the Fighter have an AC of 40
- Neither the Rogue nor the Fighter will invest into Constitution beyond 10
- Neither will they invest in the Toughness feat, or use Hit Point increasing items
- No magical items considered aside from the weapons
- Standard +4 weapons are assumed
- The Rogue has Epic Dodge
- Both build for maximum damage
- Both stay pure, meaning 30 levels in only their respective base classes
- All attacks hit, either due to Stealth (Rogue) or high AB (Fighter)
- The Rogue gets 4 attacks due to Stealthed flurry (rest won't hit due to low AB)
- The Fighter gets 4 attacks a full round, either from going first, or surviving the Stealthed flurry
- Critical hits are not taken into account
- UMD is not taken into account
Fighter
Race: Any with +2 Strength
Final Strength: 34 ----- 20 base + 14 increases
Hit Points: 300
Weapon: Greatsword (2d6)
Attacks per Round: 4 ----- 6 base - 2 from NH
Noteable Feats: Improved Power Attack, Northlander Hewing (NH), Epic Focus, Epic Specialization, Weapon Mastery, Weapon Supremacy, Epic Prowess
Total Damage: 56 to 66 ----- 2d6 + 4 EB + 18 (Str) + 8 (Mastery, Specialization) + 12 IPA + 12 NH
Due to Epic Dodge 1 of the 4 attacks does no damage.
Defensive Roll is ignored since it requires a natural 20 to succeed on a Reflex save vs a minimum DC of 56.
Therefore the damage per round will be:
183 ----- 3 x 56 to 66 = 3 x 61 average
Rogue
Race: Any with +2 Dexterity
Final Strength: 14
Hit Points: 180
Weapon: Dagger (1d4)
Noteable Feats: Epic Dodge, Perfect Two-Weapon Fighting, Improved Sneak Attack +5d6
Total Sneak Attack: 20d6 ----- 15d6 base + 5d6 epic
Total Damage: 27 to 130 ----- 1d4 + 4 EB + 2 (Str) + 20d6 (SA)
The Fighter has no special abilities to mitigate hits or damage.
Therefore the damage per round will be:
308 ----- 4 x 27 to 130 = 4 x 78 average
Summary
If the Rogue gets the jump on the Fighter the Rogue will win by dealing 308 damage to a 300 Hit Point target.
If the Fighter gets the jump on the Rogue the Fighter will win by dealing 183 damage to a 180 Hit Point target.
The Fighter has more reliable damage, both in damage range, and delivery. 56 to 66 vs 27 to 130. No Stealth vs Stealth.
Thus low damage rolls for the Rogue is more likely to result in the Fighter surviving the first round than the other way around.
Conclusion
All things being equal, and utilizing the law of averages, the Rogue is the winner.
But only by a narrow margin due to the high variance in Sneak Attack output.
Still the winner though.
Final thoughts
When taking critical hits into consideration the Fighter benefits more than the Rogue due to the above-mentioned reliability of damage rolls, and thus the balance shifts more towards the Fighter.
When taking higher Constiution, the Toughness feat, and Hit Point increases into consideration the balance shifts towards the Rogue, due to their higher damage potential still being able to Stealth flurry a target with up to 520 Hit Points (4 x 130).
For a theoretical experiment, however, the law of averages is better, and thus I stand by the semi-conclusion above.