But assassins have keen senses and would know which are bots and the real deal. Also, an assassin would sneak up on Doom and kill him before he could ever plan a way out of it.

No one can sneak up on the all powerful Doom because the all powerful Doom knows all :p

But asssassins would know Doom would know, doing an alter plan doom would never think of.

One of the things I love about VS is the way plot twists and equipment reflect the "anybody can beat anybody" mentality of comics. Using VS as a reference, let's look at both their strengths.

Ra's has...

Advanced understanding of electical brain signals.
Mastery of biological warfare.
Expertise in nature based alchemy.
A cruise ship to relax on after a hard day's scheming.
Eats children.

Doom has...

Super advanced homemade technology.
Minimal knowledge of certain occult sorceries.
A country.
Serious overcompensation issues.
Also eats children.

It all depends on which of these skills they brings to the table.