Something like:

Deck 1: Aragorn (Leadership), Legolas (Tactics), Gimli (Tactics)

Deck 2: Gandalf (Neutral), Samwise (Leadership), Frodo (Spirit)

Deck 3: Boromir (Tactics), Merry (Tactics), Pippin (Lore).

Or any combination thereof? Maybe Loragorn for threat and more lore resources to get healers on the table.

Or a 4th deck could be pure support - maybe Silvans, helping from a distance with effects and Ranged characters? Galadriel keeps threat down, Elrond adds bonus to healing, Arwen adds to someone's defense etc. But this deck refrains from directly engaging enemies unless necessary.

I attempted this while playing Road Darkens with 2 decks. Aragorn (Lore), Gimli, and Legolas for one deck and Sam, Merry, Pippin (Spirit) for the other deck. Frodo was the fellowship hero and the Hobbit deck had Boromir ally and Gandalf (OHaUH) ally. I was able to get the full fellowship on the board a couple times, but the decks were otherwise not great. I used Spirit Pippin to get access to Test of Will, Unexpected Courage, and threat reduction, but he is so vastly inferior to Lore Pippin. Gimli also ended up being fairly useless despite his high threat.

I tried something similar. I tried songs to get access to A Test of Will. Lackluster results. Not having ally versions of most of the Fellowship and some Spirit versions of the heroes really downgraded the experience for me.

I really enjoy this as a game, but not being able to use the Fellowship does take away from the gaming experience. The theme becomes a little forced when you can't play out your favorite bits effectively.

I've been successful 2-player with thematic decks so far.

Black Riders: Fatty, Glorfindel (Sp), Merry and Pippin (Lo), Aragorn (Lo), Sam. Obviously not matching with theme having all those characters right out of Frodo's house. A Knife in the Dark was the most challenging, but we had good results for each quest (multiple attempts on each).

The Road Darkens: decks changed to mono-tactics Legolas/Gimli/Merry on one end with Sam/Aragorn(Lore)/Pippin(Lore) on the other. Got through Breaking and The Ring Goes South OK (a few attempts for each), massive problems with Journey in the Dark, but survived it. Boromir and Gandalf were represented as allies.

Treason of Saruman: now we're back to the point where 2 decks are too many to capture theme. Uruk-hai quest, we had Merry/Pippin as captives. Stuck with that left Aragorn/Sam in one deck, but Aragorn became the Fellowship hero. Added Theoden(Sp) to represent Rohan's influence on this section of the books, even though he was not with the party during the chase, obviously. Sam stayed in to avoid the +1 threat, sadly. Legolas/Gimli on the other end was fine. Helm's Deep and The Road to Isengard we switched up to Erkenbrand/Theoden(Sp)/Eowyn, and Treebeard/Legolas/Gimli. Treebeard obviously being the odd man out, but wanted these decks to work for the journey to Isengard as well, so these decks are a combination of the different individuals involved in the two events being depicted here. Helm's Deep was very challenging with that lot, and required use of a couple of boons, but we did very well against Isengard.

The next box will bring a whole new set of challenges and capitulations with respect to theme. Just not that many characters around in that section of the narrative.

After we got Treason I ran the Road quests again with this line up:

Gandalf

Sam

Spippen

Loragorn

Boromir

Merry

With Gimli and Legolas as allies. This went really well. After sacrificing Gandalf in Moria I ran the first deck as a secrecy deck to finish the box. I was really satisfied with the results.