Well, if Applejack would turn into Alicorn, it would be:
Lol man, you made Twilight totally underpowered compared to Applejack, keep in mind that as strong as AJ is, Twilight is power house of the team.
Also, when Earth Ponies have much strength, stamina and endurance,
Unicorns have strong magic and much magic points,
Pegasus focus on agility and speed while still having a bit of weather control for magical attack.
Alicorn have agility of Pegasus, strength and stamina of Earth Pony but main strong point of Alicorn is magic like powered up version of Unicorn and in my headcanon also endurance to not die to they own spells.
So AJ transforming into Alicorn mean that her strength would not increase as she already was earth pony, but her magic and agility would go up ( especially magic ).
Twilight transformig into Alicorn mean she get even more magic power, but she also get buff into Strength and Agility.
As for putting points into they status, well, Twilight may be Alicorn, wings, more magic power and more strength, but since she not work as hard as AJ and never flew before, she is far behind AJ and RainbowDash, as for her magic, it is part what will improve as Twilight will train and level up.
As for AJ, situation would be worse, AJ would be able to learn magic and gain agility and speed, but since she already is Earth Pony, she will not get any more strength, and as physical fighter she would waste Alicorn stronger point, Magic, the only think AJ would gain would be extra endurance.
So yea, Alicorn seems perfect class for Twilight.