Agreed. There is no difference in abilities between the techs. You pay for performance. The clan mechs will be more expensive but they typically have higher stats. The number of units is what can cause problems.
Seconded.
PV doesn't care where your technology comes from, it only cares about how effective that tech is on the battlefield.
While its true that Clan Mechs typically have more firepower and, generally, topped out Armor stats, the InnerSphere mechs - with their Standard Engines - tend to have more Structure and thus more battlefield longevity. This "combat durability" ratio is about evenly matched between "kill in one shot" (clan equipment) and "takes forever to kill" (innersphere tech). There are plenty more tricks to shorten/lengthen an individual's combat durability (in-game Specials, scenario setup, luck, etc) but those are more detailed than the scope of the OP question.
Example: the Timberwolf "Mad Cat" [A] and an Atlas [AS7-D]. Both are 52 PV and are pretty evenly matched in my experience of both Classic and AS. Both need the same number of successful attacks at each range (respectfully) to destroy the other (6 at Long, 3 at Medium/Short). Winner is decided by luck and field conditions now :)
"Equal Numbers" is the balancing factor to "Equal PV" Similar to how tonnage caps worked in Classic, PV balancing
does work so long as the number of units on the field are
also similar. Lance vs Star or Company vs Binary or what have you. Savannah Master and Infantry swarms are just as annoying in AlphaStrike as they are in Classic. The closer the number of units per side on the table, the better the gameplay (in my opinion).
"Clan Pilots have better skills"
Another habit/stigma carried over from Classic and should be disregarded.
PV represents the
equipment potential at Regular Skill [4]; between the Timberwolf and Atlas above, both units are already evenly matched. In AlphaStrike, the pilots are abstracted; there's no difference between a homegrown Sphereoid and trueborn creche.
If a player/gamemaster insists on enforcing the roleplay between I.S./Clan, then they should build their forces to include the PV differences or find other means of balancing forces (justly).
Example: instead of a Timberwolf [A] at Skill 4 for 52 PV, the controlling player could field a Timberwolf [ B] at Skill 3 for 53 (base 44 PV, +9 for Skill up) and still be evenly matched against the Atlas AS7-D at Skill 4.