Edit: This answer predates several rulings and clarifications made by WotC and Crawford in particular. I'm leaving it in place for historic purposes, but it's no longer a particularly useful answer.
Strictly speaking, there is no clear interpretation. All three cases are justifiable. Also note that 5e discourages literal "rules as written" meanings. As the designers have repeatedly said: "rulings, not rules." The rules were explicitly not written to be scrutinized as a lawyer scrutinizes the law, so we should not be surprised when the end result of "it's ambiguous" is what we find.
Firstly, "natural" melee weapons are, as far as I'm aware, considered melee weapon in 5e. [ See also.] There is no distinction between a mace and a hoof as far as "counts as a weapon" is concerned in 5e. I don't know if this is explicitly stated anywhere (I thought it was) but Unarmed Strike is explicitly listed as a weapon on the weapons table, and it's strongly implied since all monster stat blocks say things like "Bite Melee weapon attack: [...]". As far as I can tell, if you make an attack with it, it's considered a "weapon" in 5e. Something is a weapon if it's used to make an attack, then, not because it's got a weapon tag on it.
You could argue a Case 1 by saying that find steed only modifies the target of the spell. The spell still refers to "you," so even though it effects your mount, that extension does nothing. In other words, you argue that for Range: Self spells, "you" in the spell description means exactly, "you, the spell caster," and never, "you, the spell's target." This interpretation, however, also modifies spells like divine favor, detect evil and good, crusader's mantle (that one's a bit of a pickle to decode with a mount), and every other Range: Self spell. I'd argue it's all or nothing here. Either they all work on the mount (in some way), or none of them do. It doesn't matter how you rule here, but you should be consistent. Given the number and range of Paladin spells that are Range: Self I question an interpretation this narrow as being the design intent, but it's certainly supportable. About the only thing that reinforces this interpretation is the fact that the Smite class ability does not work on a find steed mount, but that's only because the class ability isn't a spell so it doesn't qualify for find steed's expansion.
The difference between Case 2 and Case 3 is deciding if find steed changes the wording of spells to "The first time both you and your mount hit with a melee weapon attack [...]" or changes to "The first time either you or your mount hit with a melee weapon attack [...]". Honestly, there's not enough information to decide either way. The spells are not written with find steed in mind, and find steed is not worded to make the end result clear.
You can argue Case 2 by saying, "The spell is intended to only affect a single melee attack; if it were intended to affect multiple targets, it would be higher level or otherwise deal less damage."
You can argue Case 3 by saying, "Find steed, like find familiar or hunter's mark, is a class ability masquerading as a 2nd level spell, and that wording was put there to have an intended effect. Furthermore, making a Paladin more deadly while mounted -- a fairly rare situation in most campaigns, IMX, and small Paladins are already less threatening -- is in-line with the desired result of the theme and flavor of the class. Given also the relative scarcity of spell slots, the additional power is probably not significant in most cases." This is not a particularly crunchy argument, but given that 5e does not separate crunch and fluff, it is legitimate.
If I were to rule conservatively, I would probably rule Case 2. If I were in a more liberal frame of mind, Case 3 would be reasonable. As it stands, I don't see any compelling justification for any one interpretation.
Best Answer
It means exactly what the spell says
So it's apparently well-accepted that "5e has no flavour text". Fine; I'm not personally sure that's actually true, but let's assume it is. Every part of that spell text is meaningful in that none of it describes something that isn't actually happening in the game. You definitely have an "instinctive bond" with your mount and can fight with it as a "seamless unit". What does that mean?
Let's look at another example. Here's the paladin's Divine Sense ability:
Here's an excerpt from twitter showing us what the author of the rules has to say about how to read them, in the context of interpreting the paladin's Divine Sense ability:
Here Jeremy Crawford explains that often, the rules are written such that one sentence may say a thing and then the following sentences explain what that first sentence meant, providing context and clarification. Divine Sense says a thing that is vague - paladins can sense strong evil and powerful good - and then immediately explains what it actually means when it says that. The fact that the ability is actually more restricted in scope doesn't make the first sentence not true (i.e. "flavour text"); paladins can detect certain kinds of evil and good.
This is the exact same sort of text as in find steed.
You have an instinctive bond with your mount that allows you to fight as a seamless unit. What does fighting as a seamless unit mean, in this context? It means that you can affect yourself and your mount with certain spells as if you were a single person, both enjoying the benefit of a spell that normally would only affect you as an individual; one might almost say the spell observes no seam between you and your mount.
This isn't a circumstance where the rules say a vague thing and then don't explain it and we have to figure out what it means; this is a circumstance where the text immediately explains itself. You are not meant to try and infer some kind of extra benefit beyond what the spell itself explains about how it works.