After rewatching The Return of the Elementals, here's my (unasked for) take on Eli and Will's bond.
(This will be rather long, so fyi the last paragraph gives you an idea of my point)
The obvious premise is that it's a kid-friendly show, so none of this could be explored canonically. But if Slugterra were aimed at teen and up audiences, I think there would be some really interesting dynamics to be shown. So bear with me as I speculate over between-the-lines stuff.
First of all, I think ROTE went deeper than expected. We see Eli finding out that his father is not only not dead, but also very much possessed, by the very being that once had haunted his own mind. We're talking about years and years of grieving and coming to terms with Will being gone, all undone by a single realization. That must have been *way* more traumatic for Eli than a simple frown and mild shock.
But no, Will simply gets down to business and asks Eli to update him about the current situation with the Elementals, when it would have taken even just a look, a touch, a pat on the back to acknowledge that yes, he had missed his son, he was proud of him; that yes, in a few words, he loved him. It wouldn't have been time wasted not saving Slugterra: I'm talking about little things, which, when it comes to family, more often then not are all is needed.
Because duty must be paramount to a Shane of course, and both Will and Eli understand that (Will being super paranoid and preparing letters and messages for Eli shows that; Eli delaying rescuing him later on in favor of more urgent business also points in that direction). But honestly, once you decide having a family, isn't being the best dad possible to your son just as much a duty? Seing Will be so emotionally sterile towards Eli during their very first meeting after years, especially in an apocalyptical context, made my heart ache.
Indeed, on the recieving end of this non existent affection display, we have Eli, who is not only bearing the huge responsibility of literally saving the world, but also an even greater one: showing his dad that he can be proud of "the man he has become". This is unexplored terrain in the series, but I don't think it's a far fetched guess to say that Eli is very concerned with living up to what might have been his father's expectations, and stay with me here. We are talking about someone who's been groomed since he was born to potentially become a hero, part of a long generational line. He canonically clearly idolizes Will, and he always blames himself first when things go wrong. His role calls for excellency, and that's something Eli's clearly okay with.
My point though is that I think these convictions about who he should be led Eli to accept that pride is a necessary condition for love. That fatherly love must be earned through success, through the very prioritising of duty over everything else. Why else wouldn't he have not batted an eye when Will himself didn't do so at their first reunion after years?
To summarize what I mean, think about the last scene in Into the Shadows. Will has a message for Eli to give him his birthday wishes: this shows he did indeed care for his son. But, after a few words, he literally turns his back on him, and Eli is left dealing with his emotions and the fact that he misses Will by himself. I think this was the pattern in their relationship: surface connection (pun unintended), but never deep enough, at least for Eli to be satisfied. Maybe Will purposefully avoided it to make their goodbyes easier, or maybe not. Maybe Eli himself learned to close himself off to fit the "hero" role he was always told he would have taken (what I'm leaning towards). Maybe that's why he trusts people so easily (Twist, Thad, Junjie and Dana specifically): there can't be a way of actually knowing someone anyways, starting from your own biological family. Luckily enough though, Eli found a family who doesn't mind his vulnerabilities and, again symbolically enough, celebrate with cake despite of, or actually because of, Eli's acknowledgement that he misses his dad (which he didn't want them to hear anyways).
Being an INFJ I'm drawn to things like that, and I'd love to read any thoughts of yours about it.