Whether base attacks are punishments or not, imo, depends on how you view the game. If you view it as a game, then you can certainly make that argument. However, in my view, games like X-Com are meant to be simulations, and base attacks are important in that sense. As previously stated, base attacks are the AIs reaction to you. In the game, the AI should seek to win, not just be an obstacle to you winning. In a multi-player strategy game, the other player doesn't simply throw stuff at you for you to fight and stop short of defeating you. The other player will actively seek victory, and if you are impeding said victory, the player will seek to remove that threat and obstacle. The AI should be doing the same. Ideally, there would be multiple levels of AI responses like unthreatened, passive defense, active defense, and offense.
Additionally, base attacks are also there to force choices between short-term and long-term goals. For example, if you have only been using a small pool of soldiers, then every time you send them out, your base is more vulnerable. Perhaps you should rotate your squads more, so that would be less of an issue. Maybe there is an landing or terror mission happening, but your fleet has taken quite a beating and you are not quite prepared to withstand a base attack. Maybe you should let the attack happen and accept the consequences in hopes that your force will be more useful in the long run. These choices can arise because the player is vulnerable. Take away that vulnerability, the choices disappear, and the game suffers. If you insist on thinking of them a punishments, then think of them as punishments for you not being prepared or having contingency plans.
That is not to say that X-Com couldn't have done a better job regarding base attacks. Personally, I believe that the options for defending against or avoiding a base attack were just too few. You should have options to, say, use passive/active camo, move the base, use smaller and cheaper "sub bases" to allow for defense through dispersion, etc...
In terms of the soldier progression and cover systems from XCOM:EU, do not implement them like EU does. The progression system was way too restrictive. Something like a upgrade points system with multiple trees would be much better or apply abilities to weapons and not soldiers. The cover system was way too binary leading to situations where it did not make sense. If you are going to use cover, make it more complex. If a soldier is 1 square away from being 90 degrees from and enemy and flanking them, unless the enemy is really thin or there is another obstruction in the way, the enemy should not get full or any cover bonuses.