Ships & Modules

"Worst" in what way?

The two most significant limitations that I can personally think of for Amarr Alphas are:

1. Lasers only do two types of damage, EM and Thermal.
For PVE, Thermal is the most common damage weakness for NPC rats. On the other hand EM is the least common NPC damage weakness. If you want to do a lot of PVE as an Amarr Alpha, picking which NPC's you fight is something to pay attention to. On the other hand, lasers do not need to be constantly supplied with ammo like most of the other weapon systems do.

For PVP, it's much harder to give a definitive statement about damage weaknesses and what types of damage to use since players have the ability to fine tune the damage resistances of their ships with modules and rigs.

2: Amarr ships are normally armour tanked, which means using up low slots for more tank modules. Most of the modules that increase weapon damage are also low slot items, so as you put more armour modules on a ship, you have fewer slots for damage modules that give you extra dps. Gallente ships are similar, mostly armour tanked.

Drones. An Amarr Alpha can train drone skills to exactly the same level as a Gallente Alpha can. Caldari and Minmatar Alphas have significantly more restrictions on their drone skills. Both Amarr and Gallente have ships specialised for operating combat drones, although I'd personally put Gallente a bit ahead of Amarr in this detail. Amarr doesn't have a specialised drone frigate like Gallente, but from the destroyer level and going up, both Amarr and Gallente have specialised drone ships.

In terms of maximum dps, the advantage goes to the Gallente drone ships. They can fit more weapon turrets and have more drone bandwidth to control drones compared to the Amarr drone ships. On the other hand, the Amarr drone ships have ewar bonuses that the Gallente ships don't get, making the Amarr drone ships potentially very useful for PVP. NPC rats are immune to some types of ewar so in PVE the Amarr drone ships are a bit more limited.

Also, an Amarr Alpha is not restricted to using only Amarr drones, they can use any type of light or medium combat drone, giving them more options for the damage type they want to use (the same it true for Gallente Alphas). Amarr drone ships available to Alphas have larger drone bays than equivalent Gallente drone ships, meaning the Amarr drone ships can carry a larger variety of drones.

I think out of the four main empires, Gallente Alphas are in a strong position, but I'm not convinced that Amarr Alphas are in the worst position.

Amarr alphas are solid. It's just some guys forgetting about the fact that Pulse lasers don't work without Scorch try to fit some pulse laser fits, then cry about it's inefficiency.
From ancient times though, Amarrs followed simple pattern:
For small and medium lasers: Beams for t1, Scorch pulse for t2.
For large lasers: Tachs uber alles.
And while Amarrs don't have that raw DPS of gallente, they are truly the masters of actually applied damage.
For example, everyone loves hobgoblins for their dps. However, I've yet to see the day with hobgoblins NOT missing their first shot on frigate when not asssisted by ship bonuses/omnitracking modules. In fact, hobgoblins miss about 2.5 times per full flight volley untill the THIRD shot, which is already 12th second.
Acolyte does less damage, sure, but it rarely if ever misses, flies almost as fast as warrior and got more HP than hobgoblin.