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So, I'm somewhat bothered that far too often, the Fighter ends up dealing a fraction of the damage a Rogue dishes out each round. In my opinion, the Fighter should be more adept at delivering more severe blows, in the form of more raw damage, while the Rogue should perhaps not deal raw physical damage to the same extent. Therefore, I have a few suggestions in terms of class alterations for the Fighter, a complete revision of the Sneak Attack system, as well as a small modification to a few feats.

Fighter
Put your back into it
On levels 4, 12 and 20, the Fighter gains an additional die of damage to all weapons. For the purpose of weapons with multiple damage dice (such as the scythe's 2d4, or the greatsword's 2d6), this ability is not a damage multiplier, it adds 1, 2 and finally 3 dice of damage to the roll. These are simple, brute-force damage, multiplied by critical hits.
Hitting where it hurts
On levels 8 and 16, the Fighter adds 1 to all critical multipliers - a longsword advances to x3 on level 8 and x4 on level 16, for example. This explicitly stacks with other feats and class abilities.

Class Ability Change
Sneak Attack
The usual restrictions still apply, however, instead of the incremental dice of additional damage, all classes and prestige classes that deal Sneak Attack damage follow this progression:
1d6 - 1 point of Physical Ability Damage to any one physical ability.
2d6 - 1 point of Physical Ability Damage each to any two physical abilities.
3d6 - 1 point of Physical Ability Damage each to all three physical abilities.
4d6 - Melee or Ranged Style - the Rogue chooses either the Ranged Sneak Attack ability (Sneak Attack up to weapon's base range, i.e. 80 ft. for a light crossbow, for example; or up to Close Range for targeted spells - in lieu of actual caster levels, count class levels that grant Sneak Attack as caster level to determine range), or the Melee Sneak Attack ability Critical Sneak Attack (applying Sneak Attack damage to all Critical Hits).
5d6 - Improved Sneak Attack Once per day, the Rogue may double the effect of a single Sneak Attack. This must be declared before the Attack Roll.
6d6 - 2 points of Physical Ability Damage to any one physical ability, 1 each to the remaining two physical abilities.
7d6 - 2 points of Physical Ability Damage each to two physical abilities, 1 to the third physical ability.
8d6 - 2 points of Physical Ability Damage each to all three physical abilities.
9d6 - Improved Melee or Ranged Style - the Rogue gets the Sniper ability (Sneak Attack out to maximum weapon range, or up to long range for targeted spells; in lieu of actual caster levels, count class levels that grant Sneak Attack as caster levels to determine range) as a Ranged Style advance, or the Melee Sneak Attack ability Sneak Attack of Opportunity, adding Sneak Attack damage to all Attacks of Opportunity (fairly self-evident).
10d6 - Greater Improved Sneak Attack Three times per day, the Rogue may double the effect of a single Sneak Attack. This must be declared before the Attack Roll.

Modified Feats
Weapon Focus
This feat grants a +1 Attack Bonus with the chosen weapon, and an additional +1 Attack Bonus each 5 points of Base Attack Bonus, i.e. +1 at BAB 1, +2 at BAB 6, +3 at BAB 11 and +4 at BAB 16.

Weapon Specialization
This feat grants a +2 bonus to damage per bonus die of damage, i.e. +2 at Fighter level 4, +4 at Fighter Level 12 and +6 at Fighter Level 20. This damage is multiplied on Critical Hits.

Greater Weapon Focus
This feat doubles the attack bonus from Weapon Focus.

Greater Weapon Specialization
This feat doubles the damage bonus from Weapon Specialization.

I think this adjustment should render the Fighter a more viable class choice and tune down the Rogue without rendering it worthless in a fight. Thoughts? Objections? Tweaks?

Reading the description of Surprise Spells, I should argue to your DM that the Class Ability does have a purpose, even when Sneak Attack is added to spells which normally have attack rolls. Because Surprise Spells is described as follows: "At 10th level, an arcane trickster can add her sneak attack damage to any spell that deals damage, if the targets are flat-footed." The relevant part here is "any spell that deals damage" - which is, as written, NOT limited to spells which have attack rolls. Which means that you can now deal sneak attack damage with spells such as Fireball, Cone of Cold, or any other spell with an area of effect. In fact, for my personal, sadistic, sneaky favorite, Surprise Spells add Sneak Attack damage to Explosive Runes. Which, considering that the poor sot of a reader just took 7d6 additional damage on top of the 6d6 damage from the page detonating in his face. (Given that the Arcane Trickster adds 5d6 Sneak Attack damage, and has an entry requirement of 2d6 Sneak Attack.)

In short, all spells with attack rolls can have Sneak Attack added to them given the right conditions. Surprise Spells increases the range of spells to which sneak attack may be applied.