1) 自主研发力量的薄弱 = weakness of independent research and development competence
2) 薄弱的自主研发力量 = weak independent research and development competence
Both of them are acceptable. From a grammar point of view, (I'm a native speaker, but my Chinese grammar got rusty after I learned English) both of them are 偏正短语 (modified phrase?). 偏正短语 consists two parts, one could be considered the object (or subject? I'm not really sure what to call it here) of the phrase and the other part that modifies it. The object is the main part of the sentence which means if you remove the modifier, the sentence is still grammatically correct.
However, in many situations like this question, the modifier and the object can be converted back and forth. So it's more a speaker's choice. For example you can consider which of the two you want to emphasise. The first one emphasise 'weakness', the second one emphasise 'R&D competence'.