House rules should not be essential to play the game.
The only rule lacking for playability in Palladium is the rule describing how to read dice. It may not be fun, but it's definitely playable as written if one knows how to read the dice and use polyhedral dice. I've in fact run whole campaigns using Palladium Games' Fantasy and Robotech systems… which are in fact the same mechanics as rifts. Lots of stuff in the system I don't like, but it's playable as written.
Likewise, EOTE as written in the Beta book is quite playable. It has some suboptimal decisions.
First, the decision to use a class based system.
I can understand why they went with the class-based skill/trait acquisition, but in-play skill driven play. Houseruling around that is trivially simple… pick one of the following:
A) 12 career skills, 6 of them receiving 1 rank each
B) 11 career skills, 4 of them at one rank each, 1 at 2 ranks
C) 10 career skills, 2 at 2 ranks, 2 at 1 rank each.
1st 4 trait ranks cost 5 points each, and have to appear on any extant tree's 5 line.
2nd 4 trait ranks cost 10 points each, and have to appear on any extant tree's 5 or 10 line
3rd 4 trait ranks cost 15 points each, and have to appear on any extant tree's 5, 10 or 15 line.
In fact, that might make an excellent "optional rule" in the back of the book (And I'd be thrilled if it made it in.) The extant system creates archetypes that resonate with the setting and give an instant "in" to the intended styles of play. Fortunately, the system only makes class strongly valuable for trait acquisition; skill gains are only mildly impacted by not being in-class.
The second suboptimal decision in the beta is scaling. Not that it uses scales, but that it has too few. The setting includes vehicles from 1.5m to 15km long… and the simplicity of the scaling mechanic is nice, but doesn't match all the canon sources all that well. (Tho' Clone Wars may not be one that they really considered. In at least two episodes, I've seen clonetrooper carbines do damage to starfighter sized tanks… and tanks should be less fragile than starfighters of the same size.)
The third suboptimal decision is to not have operational costs and expected "normal" income for ships.
The fourth was to not have a good ratio of what a ships' cargo enc is, and relating it to the Extended Universe data already out there.
None of these are fatal flaws.
Seriously, all the decisions I've isolated as suboptimal are issues, but not ones that break the underlying system. The only truly major flaw isn't one for me - the custom dice. It's a high barrier for some people, including my wife, but in play, I have been convinced of the value in play.
And, once the big book is out, I'll be happy to houserule myself as needed… but the more houserules I need, the less likely I am to advocate for and/or use the system. (My general limit is 1 page of house rules. Possibly plus a 1/2 page list of canonical optional rules in force.) And my players tend to acquire rulebooks for systems they like when I run them.