A language independent deep learning (DL) architecture for machine translation (MT) evaluation is presented. This DL architecture aims at the best choice between two MT (S1, S2) outputs, based on the reference translation (Sr) and the annotation score. The outputs were generated from a statistical machine translation (SMT) system and a neural machine translation (NMT) system. The model applied in two language pairs: English - Greek (EN-EL) and English - Italian (EN-IT). In this paper, a variety of experiments with different parameter configurations is presented. Moreover, linguistic features, embeddings representation and natural language processing (NLP) metrics (BLEU, METEOR, TER, WER) were tested. The best score was achieved when the proposed model used source segments (SSE) information and the NLP metrics set. Classification accuracy has increased up to 5% (compared to previous related work) and reached quite satisfactory results for the Kendall τ score.