Often it's hard to decide if I want to equip an item i visualy like, or if I equip an item which I don't like that much with a custom animation or Icon.

For example we now have this beautiful CM-set (DotA-Plus) and I'd really like to use it, but the last non-immortal slot are bracers.
So if I equip the new head, the custom nova-effect is gone... I can't have both together. That sucks..

There are many more heroes and the more immortals or items in general we get, the more difficult are equipment decisions.

I know there was already an approach with kinetic gems and the system was kinda meh..

I suggest to offer a "sub-slot" for every item slot. The normal slot equips the item visualy and the new slot "overrides" the item effect. If this new slot is empty, the effect of the equipped item applies.
Example: Normal Slot -> White Sentry (CM-Immortal Staff), sub-slot for CM-Staff -> Golden Ice Blossom. This results in CM using the White Sentry and having the aura effect and spell icon of Golden Ice Blossom.
Example 2: Normal Slot -> Golden Ice Blossom, sub-slot -> empty. results in CM using the Golden Ice Blossom scepter with it's effect.
So for each item slot we have the original slot for appearence and another new slot for the effect. This way we don't even need to change the items itself, because we simply equip the effect item to the effect slot.
Effect slot should use:
- custom spell animations
- custom icons
- arcana effects
Effect slots should not use:
- particle effects

This feature could be extended by offering even more slots to seperately customize spell effects, icons, models (arcana) and so on, but I guess for now it's a much bigger implementation effort.

In my opinion this is a relativly easy method to separate effects and equipment, because there is no need to change the item database.
On valves side, this will also boost market transactions, because alot of different items will become attractive options again.
The more immortals we get, the more fixed is the current top-notch equipment for a hero, because none wants to sacrify a custom spell animation.
In fact valve only needs to double the equipment slot (minus taunt) and pick the custom effects from the new slots, while taking the visual appearence from the default slot.