Yes, werden is complex and I think part of the problem is you're trying to conflate it with "to be/was", which is equally complex but in a different way. It's best to untangle this by looking at the various uses of werden; it's often better to describe the meanings of German words independently rather then to try to match them with English words. But first, it should be noted that the sentence "The suitcase was packed," has two meanings. There is the passive meaning, saying that someone packed the suitcase without mentioning who. And there is also the descriptive meaning, saying that the suitcase was full of clothes etc. The two meanings in English have different translations in German, one with wurde and the other with war.
By itself, werden means "to become" or "to turn", in other words to transition from a state of not being something to a state of being something. The most common translation in English is "to get", at least in informal situations. For example:
- Er wird wütend. – "He's getting angry."
- Ich werde Arzt. – "I'm becoming a doctor."
- Meine Haare werden grau. – "My hair is turning grey."
In the (simple) past test these become:
- Er wurde wütend. – "He got angry."
- Ich wurde Arzt. – "I became a doctor."
- Meine Haare wurden grau. – "My hair turned grey."
Grammatically, this sense of werden is similar to sein since they are both copulative verbs, meaning they are both used to describe something with an adjective or noun. The descriptive sense of "The suitcase was packed," uses the past tense of "to be", which says the suitcase was in a certain state, that of being full of clothes. So in German this is simply Der Koffer ist gepackt, but in the past tense Der Koffer war gepackt.
There are also two ways that werden can be used as an auxiliary verb, meaning a verb that combines with a special form of another verb. Two auxiliary verbs in English are "to be" and "to have". For example when you combine them with the verb "to eat" you get "I am eating" (progressive tense) and "I have eaten" (perfect tense). Keep in mind that tenses and other verb forms usually don't correspond between languages; there is no progressive tense in German and while German does have a perfect tense, it's used differently than in English. You have to learn a set of circumstances where each tense or verb form is used, with different sets of circumstances used in each language.
One use of werden as an auxiliary verb is to form the future tense. In English this is normally done with "will" or "shall". In this case werden is combined with the infinitive of the other verb, and the infinitive is placed at the end of the sentence. In German the auxiliary verb is always conjugated, in contrast to English where "will" and "shall" aren't. When the infinitive is sein you get the various forms listed in the question. For example:
- Ich werde frei sein. – "I shall be free."
- Naomi wird Ärztin sein. – "Naomi will be a doctor."
This can be a bit confusing since werden in it's "become" meaning and sein are similar in both meaning and grammar. The wird in Naomi wird Ärztin, is the "become" meaning; "Naomi is becoming a doctor". Meanwhile the wird in Naomi wird Ärztin sein, is the "will/shall" meaning. The only difference is the sein at the end, but that changes the grammar which in turn changes the entire meaning of the sentence. Note that there is nothing to prevent werden from combining with itself in it's other meaning:
- Naomi wird Ärztin werden. – "Naomi will become a doctor."
The other use of werden as an auxiliary verb is to form the passive voice. (As RHa points out, German has two forms of passive voice. I prefer to call the one with werden the "true passive" and the other one the "false or ersatz passive".) English forms the passive voice by combining the auxiliary verb "to be" and the past participle of another verb. In addition, the subject in the non-passive form is dropped and the direct object becomes the new subject. For example "I'm giving the child a toy," becomes "The child is being given a toy." The process in German is similar except that the auxiliary verb is werden. This does not imply werden means "to be", in fact auxiliary verbs don't really have meaning; they are just a mechanism to create certain tenses and forms of other verbs. For example:
- Ich schenke dem Kind ein Spielzeug. – "I'm giving the child a toy."
- Dem Kind wird ein Spielzeug geschenkt. – "The child is being given a toy."
Note that this wird has nothing to do with either the future tense wird or the "become" wird, but the only way to tell which one is meant is to look at the structure of the rest of the sentence. If the sentence ends with an infinitive then it's probably the future tense. If the sentence ends with a past participle then it's probably the passive voice. If the sentence ends with an adjective or noun then it's probably the "become" meaning. The passive voice can be combined with the past tense by putting the conjugated form of werden in the past tense. Hence:
- Dem Kind wurde ein Spielzeug geschenkt. – "The child was given a toy."
The sentence Die Fee wurde von den Kindern gefangen, is in the passive voice, but the subject of the original sentence has been re-added using the preposition von. So:
- Die Kinder fangen die Fee. – "The children catch the fairy." (present tense)
- Die Fee wird gefangen. – "The fairy is being caught." (passive voice, someone is catching the fairy)
- Die Fee ist gefangen. – "The fairy is caught." (ersatz passive voice, the state of the fairy is that she is in captivity)
- Die Fee wurde gefangen. – "The fairy was caught." (passive voice, past tense)
- Die Fee wurde von den Kindern gefangen – "The fairy was caught by the children." (adding "the children" back in)
You might think it's odd to remove the subject by using the passive voice only to add it back in again, but this is possible in both German and English because there is a difference between the two versions. This has to do with keeping "the fairy" the center of attention. This passive form tells you what happened to the fairy while the active form tells you what the children did.
To reiterate something covered in RHa's answer, the various tenses and voices and the different meanings of werden have nothing to do with whether a pronoun or other noun appears in a sentence. For the most part, you can simply replace a noun with a pronoun in a sentence with no additional changes. German word order prefers that pronouns do not appear at the beginning or end of a sentence, but the words themselves will remain unchanged. In general, a "noun phrase" is a combination of words that refer to a thing or person, or group of things or people. They can be any degree of complexity from er to der glückliche junge Mann, der mit einem schönen Mädchen tanzt, and they are almost always interchangeable with respect to grammar as long as you keep the same number and gender. There are, of course, exceptions to this principle, but they don't occur here.
