Limun je kiseo, ali ga svejedno volim u čaju.

Because limun is the subject of the first clause: Limun je kiseo.

The subject normally goes in the nominative case, and the nominative singular form is limun.

• limun = lemon
• Limun je kiseo = The lemon is sour / Lemon is sour

Because adjectives in Croatian agree with the noun they describe in gender, number, and case.

Limun is:

• masculine
• singular
• nominative

So the adjective also appears in the masculine singular nominative form:

• kiseo = sour

Compare:

• limun je kiseo = the lemon is sour
• voda je kisela = the water is sour/acidic
• mlijeko je kiselo = the milk is sour

Ali means but.

It connects the two contrasting ideas:

• Limun je kiseo = Lemon is sour
• ali ga svejedno volim u čaju = but I still like it in tea

So ali introduces the contrast, just like but in English.

Because Croatian often leaves out subject pronouns when the verb ending already shows who the subject is.

Volim means I like. The ending -im already tells you it is first person singular.

So:

• volim = I like
• ja volim = I like

Both are possible, but ja is usually omitted unless you want extra emphasis.

Ga means him/it, and here it means it, referring back to limun.

It is the unstressed accusative singular pronoun used for masculine and neuter nouns.

So in this sentence:

• ga = it
• it refers to limun

That is why:

• ali ga svejedno volim = but I still like it

Because Croatian pronouns do not work exactly like Croatian nouns.

For nouns:

• masculine inanimate nouns usually have the same form in nominative and accusative
• so you say volim limun, not volim limuna

But for the unstressed pronoun, the accusative form is still:

• ga = him/it

So even though limun is inanimate, the pronoun referring to it is still ga.

Because ga is a clitic: a short unstressed word that usually has to stand near the beginning of the clause.

In Croatian, clitics often appear in the second position of the clause. So:

• ali ga svejedno volim

is very natural word order.

A literal word-by-word English order would not help much here, because Croatian clitic placement follows its own rules. The important thing is that ga cannot usually just go anywhere.

Here svejedno means something like:

• still
• nevertheless
• all the same
• even so

So:

• ali ga svejedno volim = but I still like it / but I like it anyway

It shows that the second idea is true despite the first one:

• the lemon is sour,
• but I like it anyway.

Because u can take different cases depending on the meaning.

Here it means in tea, with no movement involved, so Croatian uses the locative case:

• u čaju = in tea

If there were movement into something, Croatian would use the accusative:

• staviti limun u čaj = to put lemon into tea

So:

• volim ga u čaju = I like it in tea
• stavim ga u čaj = I put it into tea

Čaju is the locative singular form of čaj.

The noun is:

• nominative: čaj = tea
• locative: čaju = in tea / about tea, depending on the preposition or structure

Because the preposition u here means in, it requires the locative:

• u čaju

Yes, absolutely.

You could say:

• Limun je kiseo, ali svejedno volim limun u čaju.

But repeating limun sounds a bit heavier. Using ga is more natural because it avoids repetition:

• Limun je kiseo, ali ga svejedno volim u čaju.

That is very similar to English:

• Lemon is sour, but I still like it in tea.

Not quite.

• volim ga u čaju = I like it in tea
  
  • focus: the lemon
• volim čaj s limunom = I like tea with lemon
  
  • focus: the tea

So the sentence you were given is specifically talking about lemon and saying that you like it when it is in tea.

Because ali introduces a contrasting clause, and in standard Croatian punctuation that contrast is normally marked with a comma.

So:

• Limun je kiseo, ali ga svejedno volim u čaju.

This works much like English:

• Lemon is sour, but I still like it in tea.