The geography fits (I hate geography as I don't think it matters, but OoS does have a map that's very similar to Koholint), and fits the backstory of LA.
Koholint Island looks almost exactly like Hyrule from ALttP, as opposed to only having a few small similarities with Holodrum.
Holodrum
Koholint Island
Hyrule (ALttP)
The similarities between Holodrum and Koholint are:
* Both have a coast with a beach area
* Both have a mountainous area to the north
* Both have a desert located in the south-east
The Similarities between Hyrule and Koholint are:
* Both have their biggest cities located to the immediate west of the land (Kakariko in Hyrule is equivalent to Mabe Village on Koholint).
* Both have a mountainous area to the north (which seems to be a trend in about any Zelda game).
* Both have a forest location to the north-west
* Both have a castle in the center of the land. The castles also look very similar, with moats running around them and going southward to an area that also looks the same, which is....
* Lake Hylia and the lake area where the Catfish's Maw is located (don't remember the name here).
A few things that are shared between OoX and LA that LttP/LA doesn't have (I'm quoting Bitterlime; because a few of these things I don't remember, but I trust him
): "-Mermaid statues
-owl statues
-Desert in the east
The first one can be contributed to rehashing of already made graphics. The second is a valid point, but its just one point when the geography between LA and ALttP is closer than that of LA and OoS, as I pointed out above.
-Veran when possesing stuff looking like the form the nightmare takes inbetween changing shapes.
Idk about this one, Sign. Seems like this is scraping the bottom of the barrel for a desperate piece of evidence. I wouldn't consider this very important at all.
-blaino
-talking animals
-friendly ghosts"
Okay, we've already brought up the "reuse of old graphics". So here's another good chance to use it.
What evidence does LttP/LA have?
The only reason OoX had enemies, some bosses, and maybe some items or statues similar to LA is because Capcom had all those graphics already available to them to use. Nintendo gave them the rights to make the game... The engine they used was obviously the same, slightly improved LA engine. They also had the opportunity to use all of those graphics and things in LA if they wanted, and they obviously did. Similarities in enemies and some bosses then don't really count, IMO.
As for the similarities between ALttP and LA, well....
* Even though I don't consider Ancient Stone Tablets canon, that story does mention that after Link defeated Ganon, he left the land of Hyrule. Where else would he have went besides..... just where the backstory of LA says he went: In search of enlightenment. Thus, getting caught in the storm.
* Ganon was not threatening Hyrule in OoX. Actually, nothing was threatening Hyrule in that game. Yes, they say Link is the hero destined to appear when "peace in Hyrule crumbles". But that doesn't mean peace in Hyrule has crumbled this time, only that the hero has only been known to appear when that happened. The Triforce clearly sent Link to Labrynna and Holodrum to complete quests there because peace THERE had crumbled. Who else besides the hylian hero could complete this task?
* The LA manual says something along the lines of "after you saved Hyrule from the demonic hands of Ganon", while the japanese one is similar, sayin "saved Hyrule from the tyranny of Ganon". Ganon had no rule or tyranny over Hyrule in OoX. This goes back to my above example, or more or less explains it more. Ganon was terrorizing the people of Hyrule in ALttP using Agahnim, and turning all the guards evil and such.
* The manual of LA states that the people were afraid of Ganon's return, thus Link went on his journey for enlightenment. Why would the people of Hyrule be scared of Ganon returning in the age of OoX if he never even done anything to Hyrule? That generation probably didn't even know about Ganon enough to worry about him, seeing as how we know it was a different age from ALttP since Link did not know Zelda in OoX.
* The final Nightmare boss in LA takes the form of Agahnim and Ganon and fights just exactly like they fought in ALttP. Clearly, these forms were based off of the ALttP bosses. You could say that this Ganon was later changed to be influenced by the one from OoX, but first, Ganon in OoX fights nothing like the one in ALttP and LA, and what about Agahnim? Yes, there was a similar Agahnim boss in the Dancing Dragon Dungeon in OoS, but he was a sub-boss and obviously very unimportant. Wouldn't you think that Link's worst nightmares would take the form of his worst experiences? Which would, of course, be Agahnim and Ganon from ALttP, and even Moldorm since he was the first boss Link fought in ALttP, AND he had to fight one again in LA. His worst nightmares wouldn't be an easy sub-boss that is not different than the ones he fought before and after him.
* The obvious intent of the game being a direct sequel to ALttP upon release, whereas in order to fit OoX into a prequel to LA, you have to take loopholes and make a lot of assumptions that are not made clear in the game or manual itself. LA is a much more clear sequel to ALttP's events than those of OoX.