Aside from, "Because the Scriptwriter said so" it would be for several reasons:

1. Due to how suddenly the Garlean Empire started conquering places something like what, 88 years ago in game? They haven't had the time to really, fully integrate all of the nations brought under their yoke into being fully loyal. This means they have to have occupational forces in every corner of their empire.

2. Since the Emperor is worshipped as a god, the position is highly coveted. This is by Emet-selch's design, in order to make succession as chaotic as possible. He was their first emperor, and he didn't name a successor on purpose to initiate a power vacuum feud. This means that since 2.1 the Garlean Empire has been fighting itself, even after Varis took up the mantle, personal feuds persisted such that Legati that should have been assisting one another in various imperial endeavors would not. The Empire is not unified, by any stretch of the imagination, and empires that get that big are historically unstable.

3. There's large concern by the Eorzean Alliance in the ARR storyline with regards to the Empire marshalling its strength and taking an interest in conquering Eorzea again. The leader NPCs even admit that if the Empire could unify just a few legions, then they could take Eorzea with little difficulty. The Empire can't though, for the aforementioned reasons.

4. Poor resource management. The Empire seems to be obsessed with spectacle and giant dreadnaught style battleships, as evidenced first by the Agrius (Midgardsormr done did sink it), and then again later with the Gration in Heavensward (Ysayle done did force it to dock with Azys Lla, seemingly permanently). These were to be the bulk of their overwhelming show of force and power, intended to stop opposition before it began. They put almost all of the manufacturing eggs into these baskets at the time, when they would have been better served by doing what they're doing now, tailing us with spies and bringing back the technology that we largely ignore, and then adapting it to individual mechs and new aircrafts/magitek units. They'd be better served by smaller, more maneuverable aircraft, as evidenced by just how many of the larger ships were shot down in the Ghimlyt Dark.

5. Poor allocation of equipment. Rather than equipping their soldiers with the latest and greatest, they all seem to still be using the generic Garlean armors since ARR. So the Garleans wear that Black or Red armor uniform and the grunt conscripts use the leather body outfits/halfrobes with the pot helms. Many of them do not use guns, and use melee weapons comparable to what we use. Maybe if they weren't so busy pouring almost all of their resources into giant dreadnaughts, they could outfit every foot soldier with armor comparable to Gaius's or Regula's, but they do not. Imagine if they did though, instead of fighting a legion of dudes in the equivalent of Raptorskin leather, we're fighting dudes in Magitek Cybernetic Super Suits instead.

6. They are poor tacticians. Not once have the Garleans been shown to be tactical masterminds, preferring the brute force/overwhelming force method every time. They have many talented engineers, but no talented war minds.

7. They have many defectors, including their most brilliant scientists. So, they still have really smart dudes working for them, developing new mecha and refurbishing allagan ingenuity, but they've lost Cid and Nero. They lost Cid's Dad to Bahamut. Brilliant minds are the crux of their "advantage," and without them they're left using tech that eventually breaks down. Imagine having to try and use the same car for as long as you possibly could without anyone to properly maintenance it. A lot of Garleans believe themselves above that sort of work too, even conscripts, and they attempt to force it on peasant folk as well. For as dangerous as Magitek can be, it still has the inherent limitation that all machinery does. Needs maintenance and fuel.

8. The intrinsic limitation of Magitek - It can be used by almost anyone. Magitek devices are built to be user friendly. Just about anyone can repurpose it for their own needs, and just as we've seen with us stealing a Magitek Reaper or more recently, the Bozjan Resistance repurposing a Tunnel Armor, if you do manage to defeat Garleans, then you can steal their tech, completely absconding with their "advantage."

9. There don't seem to be any Garlean boot camps or training programs for conscripts: Conscripts are given a few options. Either you know how to fight and get shipped off to fight, or you don't, and you get forced into a logistics/maintenance oriented role. You are given training for neither. This does not make for a strong army.

10. Garleans care not for Aethereytes. They can't use them, not the purebloods, and even those who can use them, the Conscripts, do not get to use them. Exceptions would lie with non-pureblood spies. When they conquer an area, the Garleans do not destroy the aethereytes. In fact, they seem to leave them completely unmolested. It's as if they do not know what they are for, at all. You'd think that they'd have the most basic of tactical acumens and could at least make them priority targets during war, but nope, they don't do jackshit against aethereytes.

11. Next to no Naval power. It's said that there are Garlean ships about that the Limsan privateers and pirates often perform raids on, and we know that Ceruleum engines can be used to make travel by ship far faster, but we're never shown any Garlean examples. Yet, we live in a world where deep sea submersibles are commonly made, even by players, so where the hell is the Garleans' Navy? You'd think they'd have developed aircraft carriers by now, so that they don't have to always fly over land to and from the Garlean capital, constantly wasting so much Ceruleum. If they can make something like the Agrius or the Gration fly, then there's no reason that they couldn't make something like them that floats. They could have one for each major coast, and it'd cut their fuel expenditures for their airships by so much that they'd pay for themselves.

12. No modern equivalent of artillery. The closest thing we get is that big ass cannon in Stormblood that Estinien disables. If they had proper long-range artillery though, then they'd be far more effective at winning land battles. Hell, if they'd had proper artillery mounted on Ala Mhigo's ramparts, then breaching those front gates would have been nigh impossible for the resistance.

Basically, the short of it is, the Garleans seem super advanced because of their weird sci-fi fantasy tech, but they're actually fairly simplistic and still controlled by a primitive, braindead leadership. To them, technology is more or less a big cudgel.