I think it may depend on what you're following that phrase with. Usually when i say something had been I say Había estado but thats like if I say Había estado janguin con sus panas antes de ir al cine.( He had been hanging out with his friends before he went to the movies) which is conditional... u may need to use había sido... I guess it would depend if your following that phrase with a conditional description or a description of the very nature/essence of science. I say more than likely u will need habia sido... Pero no sé... se depende.

la ciencia siempre habia sido

Certainly not "estar". You didn't provide enough context to make clear why your English sentence uses "had" instead of "has". For example, if you want to say that "until something happened" (a change took place) science was his main interest, as opposed to "science has always been his main interest". In the first case you suggest that science is no longer (but was, at one time) his main interest while in the latter, it continues to be his main interest.

If you want to classify or define, you should use "ser". Otherwise, it is something circumstancial, and you use "estar".

• La ciencia es divertida - classification
• La ciencia está preparada para el futuro - circumstances

So, what's the full sentence, then?

if it's ser it has to be used with a noun

if it's estar it has to be used with an adjective

I don't know why you couldn't use any applicable adjective in this case

a mí la ciencia siempre me habia estado confusa. (putting aside the has/ had)

if it's ser it has to be used with a noun

Careful with this! If it is a noun, you have to use "ser", but if you use "ser", you don't necessarily have to use a noun:

Soy simpático (adj)

Having a noun implies that "ser" must be used, but the reverse is not automatically true. All you can say here is that if you are not using "ser", it cannot be a noun. These are called sufficient and necessary conditions in logic.