That said, as has been pointed out before, morale can be overcome or even ignored quite succesfully. The one change I might suggest is that it seems more logical for % mods to affect the flat positive morale portion prior to subtracting out the negatives. Otherwise the % buildings are effectively gated by the presence of sufficient flat morale bonusses.
I'd just ditch the negative value on LEP and replace it with a % tbh (or scrap it and use maintenance, which is a much better option). Everything else about morale is based on percentages; even the whole numbers granted are eventually converted into a percentage. This would at least allow large empires to counter it 'naturally' through capturing relics etc.
As to the relative value of patriotic; I've never taken it. I run an extreme low-morale system, since I'd rather have the +2 points from Discontent to spend on something that genuinely useful, so eliminating LEP doesn't matter. My morale will be in the toilet anyway, but the effects will largely be cancelled out by my other traits. I usually roll with Prolific (the free population is worth much more than the reduced LEP) and Engineers (since it allows me to massively boost a single shipyard when required). Taking Patriotic is largely just another sign that Marigoldran's min-maxing skills are not all they're cracked up to be, and that the game is really rather easy to break; I largely picked the same colony-spam strategy on my first play-through because that's always the best starting play in a 4x. I wasn't bothering with the exponential growth thing - I actually built up my new colonies and spread them between industrial, research and economy worlds. I was literally stunned when I eventually bumped into an enemy empire and they had half as many worlds as me, and couldn't believe that I was making over 1000bc a turn from only a few immature economy planets.
I've never really seen the race Marigoldran makes as overly optimal - he's wasting a ton of his racial points on range extensions he doesn't need (since he's colonizing everywhere) and morale and growth improvements which aren't really useful. In truth, from a brutally min-max point of view, there's plenty of dump-stat traits; morale can be safely jettisoned it's not worth preventing it collapsing anyway, growth is barely worth caring about either since the base is so low that percentages aren't effective(and using Prolific more or less removes the need for it, while taking synthetic totally eliminates it); resistance is more or less futile (badum-tish) since the planetary invasion maths is hilariously skewed in favour of the attacker, economy is next to worthless because cash is so easy to produce, trade and tourism ditto, and range doesn't matter much unless you're using really, really sparse settings, so you can pick up 14-16 points to spend on other things without really facing any problems (depending if you decide to dump Brutal, since once again the invasion mechanics are insanely favourable to the attacker anyway). That more or less allows you to pick +2 in everything else.
This is all just from poorly balanced mechanics. Changing the AI will in no way improve these traits; nor will buffing or nerfing them. Picking to dump them plays on the fact that you can quite safely choose to completely ignore about half the basic mechanics in the game and still play successfully at present, because they don't really work properly.