The following is taken directly from Thomas Stockton's ultimate score calculation guide:

Screenshot 2015-05-30-00-01-18

So I spent a bunch of my inbox energy refills today trying to determine how the game calculates your score and here are the findings:

Every meter run is worth half a point.

Every vial collected is worth 4 points.

Every boss defeated is worth 5000 points.

Combos are calculated in an increasing 5-tier fashion as follows:

Tier 1: Combos 1-10 are worth 20 points each.

Tier 2: Combos 11-20 are worth 40 points each.

Tier 3: Combos 21-30 are worth 60 points each.

Tier 4: Combos 31-40 are worth 80 points each.

Tier 5: Combos 41 and up are worth 100 points each.

All of these values are ultimately multiplied by your total team multiplier to arrive at your final score. Thus the formula for your final score is:

Score = [(M*0.5) + (V*4) + (B*5000) + (C1*20) + (C2*40) + (C3*60) + (C4*80) + (C5*100)]*T

Where: T = Team multiplier, M = Meters run, V = Vials collected, B = Bosses defeated, C1-C5 = Combos earned at tiers 1, 2, 3, 4, or 5.

Some analysis:

Defeating a regular enemy or smashing through a barrier with Web Hammer is worth 10 vials plus your combo value. Therefore it is a minumum of 60 points and a maximum of 140 points. At tier 5 combo value, defeating 7 enemies is like running 2000 meters.

You need to collect 15 vials to equal one defeated enemy with tier 1 combo counter. You need to collect 35 vials to equal one defeated enemy with tier 5 combo counter.

A defeated boss is worth 10,000 meters of running or collecting 1250 vials.

Getting 80 combos without losing your counter is worth 6000 points (1000 more than a defeated boss).

Getting 80 combos in two sets of 40 is worth 4000 points (1000 less than a defeated boss).

Getting 80 combos in 4 sets of 20 is worth 2400 points (less than half of a defeated boss).

Getting 80 combos in 8 sets of 10 (never reaching tier 2) is worth 1600 points.

This means constantly losing your combo can cost you almost 75% of the points you would have had from combos.

Ability Analysis:

+10% bonus to vials collected: Every vial you would normally pick up is worth 4.4 points. The bonus here is you actually get more vials added to your account.

+30% score from collecting vials: Every vial you pick up is worth 5.2 points. This is obviously better than the previous ability from a strictly score point of view.

Enemies give 30% more vials: Every attack gets you 13 vials instead of 10. This is 52 points vs 40 points. This is the same score bonus as the previous one but only from attack vials. Conversely, you get to keep more vials. How this compares to +10% Vial Count depends on how often you are defeating enemies vs collecting them on the ground.

30% greater score from running: Every meter is worth .65 points. If you run 20,000 meters you earn an extra 3000 points. Keep in mind you likely face 3 bosses in that distance.

+40% bonus score from defeating boss: Every boss kill is worth an extra 2000 points for a total of 7000. Compared to the bonus for running, you'd likely have earned an extra 6000 points from 3 bosses by the time 20,000 meters comes around (vs 3000 points for the running bonus).

+30% bonus score from combo counters: The 5 tiers end up being worth 26/52/78/104/130 respectively. That perfect 80 combo sequence goes from being worth 6000 points to 7800 points. This affects all the types of combos (hit, SHIELD, near miss, ring and dodge).

+1 to ring combo: AKA, double ring combos. Rings are by far less frequent than Hit and Near-Miss opportunities. This is likely worse than even the +30% to combos.

+1 to near-miss combo: These are available constantly, but they are also the most dangerous form of combo. Assuming perfect play, this is the best ability (especially after they split SHIELDs and Attacks into two different types of combo). It's obviously worth double compared to any sequence of all Near-Miss combos so a perfect 80 Near-Miss string is worth 12,000 points compared to 6,000 which is more than a defeated boss.

+1 to attack combo: This doubles your combos from hits. This includes normal enemies and the hits you rack up on the boss once you defeat him (it used to include SHIELDs but that was split to its own ability in Update 3). Counting nothing else, a defeated boss averages +10 hits upon defeat (I've gone to 12 or 13 before with furious tapping). That's +1000 points to a defeated boss at tier 5. It's also terrific when you have a Web-Hammer active since all the barrier-bashing is worth double. This is the second best scoring ability behind +1 to Near-Miss.

+1 to S.H.I.E.L.D. bomb combo: This was split off from +1 to Attacks in update 3. Consequently, it nerfed the +1 to Attacks. It's still a good ability, just not great, and it's only active during bosses. Compared to +40% for boss K.O.'s you need 20 SHIELDs at full combo to break even (which means in regular events with 12 SHIELDs per boss it is worse). It shines more in the extended boss fights found on Day 7 of multi-day events.

Combo Counter Starts at 10: This actually gives you all 10 combos on the first combo attempt which means it's worth 200 total points rather than 20. If you lose combo a lot, this could be an ok ability. It's best used to score the initial 10 combos for 200 points, avoid any further combos until the counter expires and then combo again for another 200 points. Overall a pretty weak ability.

+4 seconds to combo counter: This are a little more relevant if you lose you combo counter at tier 1 or 2 often. Maintining combos is important for maximising scoring. At high levels of play, this ability, and the Combo counter starts at 10 ability add nothing to your score and therefore should be considered very weak abilities.