I updated the instructions on page 14 on how to use the python program. If you find that one too intimidating, however, there's still this sheet, which is excellent for pairing off units and much quicker and easier to use (just copy and paste units from the Output spreadsheet I uploaded, set the range and skill levels if you want, and press Go):
https://drive.google.com/file/d/0BxH6vkK1TLalRTNxcVZ0WWJGaGMHera:
4" Armour 15, Structure 10 7/7/3 OV 2, LG
Kodiak II:
8" Armour 10, Structure 5 9/9/6 OV 2
Kodiak can decide the range. At long the Kodiak needs 7s (about three hits every five rounds), while the Ares needs 9s (about two hits every seven turns).
Mathematically, at long range we're looking at about 3.5 damage a round for the Kodiak, and 0.8331 damage a round from the Hera. At that rate, the Kodiak starts inflicting criticals on the Hera on round 5, while by the same time the Hera has done only 3-6 damage. Generally, the Hera will lose at long range. Of course, you're not always going to have the luxury of dueling across the battlefield at long range, and at medium it works out differently.
Still, I think you're right that there's a disparity. The problem is that, while the system does take LG's to-hit penalty into account, it only does so to the point where the unit's defense mod drops down to 0. In other words, if the unit's defense modifier hits 0, the system stops. However, at the tabletop the penalty from LG/SLG/VLG is still applied to a unit even if it has 0 TMM, so that effectively it has -1 defense, and that's definitely worse than 0. PV need to take this into account somehow.
Cheers for pointing this out. Thanks to you, a correction will make it in.