Generally speaking, the Outcome of a given battle is the same as it is in Classic/Standard/TotalWarfare ...so long as the PVs and total unit counts are equal (for example: a 12 mech Company vs 10 mech Binary is the standard here in my corner of the world)
In addition, room to maneuver is crucial. 6 ft x 4 ft (roughly 180cm x 120cm) seems to the the golden standard for skirmisher/war games, though if you have fewer units to field, you can get by on smaller areas.
A few things to note:
...
So my ideas what I could have done wrong:
Skill level of Clan Mechs to good? (0-2) but PV costs are equal (438x423) with advantage in numbers and PV for IS
Armor "restores" after shooting is done? (I think I remember somewhere to have read something like this....and it was something related with BT but I don't find anything in the Alpha Strike rule book)
Missile and "scatter" weapons need to be handled different - Mechs with LRMs seem to be to strong in Alpha Strike when compared with their performance in CBT.
Skills. Remember that the default cost of a unit is treated as if the Pilot were a "Skill 4" ; if you insist on increasing the Skill of a unit, always,
always make sure you charge the unit the appropriate amount of PVs. (AS Force Builder on the MasterUnitList does this for you, or it can be manually done using the table found in the
Errata.) Checking PVs throughout the entire process will help keep totals close (if not identical). It also helps to be willing to swap out a different variant or model in the event you cannot keep the PVs close enough.
Armor. Once it's gone, its gone. Armor does not restore at all unless you're playing/running in a campaign play... and even then, it can only be repaired in between scenarios/battles.
"Missiles and Scatter Weapons making Mechs too powerful" ? This sounds like you're adding the LRM Special to damage... which you should *not* be doing. "LRM1/2/2" is used for Special Munitions such as Smoke or NARC or other appropriate ammunition types; their values are merely present in the Specials section of the card in the event you wish to play with those Advanced Rules.
You will see AC/SRM/LRM Specials mostly on InnerSphere units. Most Clan units tend to utilize Streak or Artemis equipment early in their introduction years, so those specials are rare. (Clans will almost never have the AC special since the LBX and Ultra versions completely phased out the Standard Autocannon.).
Hope this helps.